Date: (Sun) Jun 28, 2015

Introduction:

Data: Source: Training: https://courses.edx.org/asset-v1:MITx+15.071x_2a+2T2015+type@asset+block/parole.csv
New:
Time period:

Synopsis:

Based on analysis utilizing <> techniques, :

Regression results: First run: : OOB_RMSE=<0.4f>; new_RMSE=<0.4f>; =; =

Classification results: First run: : Leaderboard: newobs_tbl=[0=, 1=]; submit_filename= OOB_conf_mtrx=[YN=, NY=]=; max.Accuracy.OOB=; opt.prob.threshold.OOB= =; =; =; =; =; =;

Prediction Accuracy Enhancement Options:

  • import.data chunk:
    • which obs should be in fit vs. OOB (currently dirty.0 vs .1 is split 50%)
  • inspect.data chunk:
    • For date variables
      • Appropriate factors ?
      • Different / More last* features ?
  • scrub.data chunk:
  • transform.data chunk:
    • derive features from multiple features
  • manage.missing.data chunk:
    • Not fill missing vars
    • Fill missing numerics with a different algorithm
    • Fill missing chars with data based on clusters
  • extract.features chunk:
    • Text variables: move to date extraction chunk ???
      • Mine acronyms
      • Mine places
  • Review set_global_options chunk after features are finalized

[](.png)

Potential next steps include:

  • Organization:
    • Categorize by chunk
    • Priority criteria:
      1. Ease of change
      2. Impacts report
      3. Cleans innards
      4. Bug report
  • all chunks:
    • at chunk-end rm(!glb_)
  • manage.missing.data chunk:
    • cleaner way to manage re-splitting of training vs. new entity
  • extract.features chunk:
    • Add n-grams for glb_txt_vars
      • “RTextTools”, “tau”, “RWeka”, and “textcat” packages
    • Convert user-specified mutate code to config specs
  • fit.models chunk:
    • Prediction accuracy scatter graph:
    • Add tiles (raw vs. PCA)
    • Use shiny for drop-down of “important” features
    • Use plot.ly for interactive plots ?

    • Change .fit suffix of model metrics to .mdl if it’s data independent (e.g. AIC, Adj.R.Squared - is it truly data independent ?, etc.)
    • move model_type parameter to myfit_mdl before indep_vars_vctr (keep all model_* together)
    • create a custom model for rpart that has minbucket as a tuning parameter
    • varImp for randomForest crashes in caret version:6.0.41 -> submit bug report

  • Probability handling for multinomials vs. desired binomial outcome
  • ROCR currently supports only evaluation of binary classification tasks (version 1.0.7)
  • extensions toward multiclass classification are scheduled for the next release

  • Skip trControl.method=“cv” for dummy classifier ?
  • Add custom model to caret for a dummy (baseline) classifier (binomial & multinomial) that generates proba/outcomes which mimics the freq distribution of glb_rsp_var values; Right now glb_dmy_glm_mdl always generates most frequent outcome in training data
  • glm_dmy_mdl should use the same method as glm_sel_mdl until custom dummy classifer is implemented

  • fit.all.training chunk:
    • myplot_prediction_classification: displays ‘x’ instead of ‘+’ when there are no prediction errors
  • Compare glb_sel_mdl vs. glb_fin_mdl:
    • varImp
    • Prediction differences (shd be minimal ?)
  • Move glb_analytics_diag_plots to mydsutils.R: (+) Easier to debug (-) Too many glb vars used
  • Add print(ggplot.petrinet(glb_analytics_pn) + coord_flip()) at the end of every major chunk
  • Parameterize glb_analytics_pn
  • Move glb_impute_missing_data to mydsutils.R: (-) Too many glb vars used; glb_<>_df reassigned
  • Replicate myfit_mdl_classification features in myfit_mdl_regression
  • Do non-glm methods handle interaction terms ?
  • f-score computation for classifiers should be summation across outcomes (not just the desired one ?)
  • Add accuracy computation to glb_dmy_mdl in predict.data.new chunk
  • Why does splitting fit.data.training.all chunk into separate chunks add an overhead of ~30 secs ? It’s not rbind b/c other chunks have lower elapsed time. Is it the number of plots ?
  • Incorporate code chunks in print_sessionInfo
  • Test against
    • projects in github.com/bdanalytics
    • lectures in jhu-datascience track

Analysis:

rm(list=ls())
set.seed(12345)
options(stringsAsFactors=FALSE)
source("~/Dropbox/datascience/R/myscript.R")
source("~/Dropbox/datascience/R/mydsutils.R")
## Loading required package: caret
## Loading required package: lattice
## Loading required package: ggplot2
source("~/Dropbox/datascience/R/myplot.R")
source("~/Dropbox/datascience/R/mypetrinet.R")
source("~/Dropbox/datascience/R/myplclust.R")
# Gather all package requirements here
suppressPackageStartupMessages(require(doMC))
registerDoMC(4) # max(length(glb_txt_vars), glb_n_cv_folds) + 1
#packageVersion("snow")
#require(sos); findFn("cosine", maxPages=2, sortby="MaxScore")

# Analysis control global variables
glb_trnng_url <- "https://courses.edx.org/asset-v1:MITx+15.071x_2a+2T2015+type@asset+block/parole.csv"
glb_newdt_url <- "<newdt_url>"
glb_out_pfx <- "template2_"
glb_save_envir <- FALSE # or TRUE

glb_is_separate_newobs_dataset <- FALSE    # or TRUE
    glb_split_entity_newobs_datasets <- TRUE   # or FALSE
    glb_split_newdata_method <- "sample"          # "condition" or "sample" or "copy"
    glb_split_newdata_condition <- NULL # or "is.na(<var>)"; "<var> <condition_operator> <value>"
    glb_split_newdata_size_ratio <- 0.3               # > 0 & < 1
    glb_split_sample.seed <- 144               # or any integer

glb_max_fitobs <- NULL # or any integer                         
glb_is_regression <- FALSE; glb_is_classification <- !glb_is_regression; 
    glb_is_binomial <- TRUE # or TRUE or FALSE

glb_rsp_var_raw <- "violator"

# for classification, the response variable has to be a factor
glb_rsp_var <- "violator.fctr"

# if the response factor is based on numbers/logicals e.g (0/1 OR TRUE/FALSE vs. "A"/"B"), 
#   or contains spaces (e.g. "Not in Labor Force")
#   caret predict(..., type="prob") crashes
glb_map_rsp_raw_to_var <- function(raw) {
#     return(log(raw))
    ret_vals <- rep_len(NA, length(raw)); ret_vals[!is.na(raw)] <- ifelse(raw[!is.na(raw)] == 1, "Y", "N"); return(relevel(as.factor(ret_vals), ref="N"))
#     #as.factor(paste0("B", raw))
#     #as.factor(gsub(" ", "\\.", raw))    
}
glb_map_rsp_raw_to_var(c(1, 1, 0, 0, NA))
## [1] Y    Y    N    N    <NA>
## Levels: N Y
glb_map_rsp_var_to_raw <- function(var) {
#     return(exp(var))
    as.numeric(var) - 1
#     #as.numeric(var)
#     #gsub("\\.", " ", levels(var)[as.numeric(var)])
#     c("<=50K", " >50K")[as.numeric(var)]
#     #c(FALSE, TRUE)[as.numeric(var)]
}
glb_map_rsp_var_to_raw(glb_map_rsp_raw_to_var(c(1, 1, 0, 0, NA)))
## [1]  1  1  0  0 NA
if ((glb_rsp_var != glb_rsp_var_raw) & is.null(glb_map_rsp_raw_to_var))
    stop("glb_map_rsp_raw_to_var function expected")
glb_rsp_var_out <- paste0(glb_rsp_var, ".predict.") # model_id is appended later

# List info gathered for various columns
# <col_name>:   <description>; <notes>
# male: 1 if the parolee is male, 0 if female
# race: 1 if the parolee is white, 2 otherwise
# age: the parolee's age (in years) when he or she was released from prison
# state: a code for the parolee's state. 2 is Kentucky, 3 is Louisiana, 4 is Virginia, and 1 is any other state. The three states were selected due to having a high representation in the dataset.
# time.served: the number of months the parolee served in prison (limited by the inclusion criteria to not exceed 6 months).
# max.sentence: the maximum sentence length for all charges, in months (limited by the inclusion criteria to not exceed 18 months).
# multiple.offenses: 1 if the parolee was incarcerated for multiple offenses, 0 otherwise.
# crime: a code for the parolee's main crime leading to incarceration. 2 is larceny, 3 is drug-related crime, 4 is driving-related crime, and 1 is any other crime.
# violator: 1 if the parolee violated the parole, and 0 if the parolee completed the parole without violation.

# If multiple vars are parts of id, consider concatenating them to create one id var
# If glb_id_var == NULL, ".rownames <- row.names()" is the default
glb_id_var <- NULL # or c("<var1>")
glb_category_vars <- NULL # or c("<var1>", "<var2>")
glb_drop_vars <- c(NULL) # or c("<col_name>")

glb_map_vars <- NULL # or c("<var1>", "<var2>")
glb_map_urls <- list();
# glb_map_urls[["<var1>"]] <- "<var1.url>"

glb_assign_pairs_lst <- NULL; 
# glb_assign_pairs_lst[["<var1>"]] <- list(from=c(NA),
#                                            to=c("NA.my"))
glb_assign_vars <- names(glb_assign_pairs_lst)

# Derived features
glb_derive_lst <- NULL;

# Add logs of numerics that are not distributed normally ->  do automatically ???

glb_derive_lst[["state.fctr"]] <- list(
    mapfn=function(state) { return(as.factor(state)) }
    , args=c("state"))    
glb_derive_lst[["crime.fctr"]] <- list(
    mapfn=function(crime) { return(as.factor(crime)) }
    , args=c("crime"))    
#     mapfn=function(Rasmussen) { return(ifelse(sign(Rasmussen) >= 0, 1, 0)) }
#     mapfn=function(PropR) { return(as.factor(ifelse(PropR >= 0.5, "Y", "N"))) }
#     mapfn=function(Week) { return(substr(Week, 1, 10)) }
#     mapfn=function(raw) { tfr_raw <- as.character(cut(raw, 5)); 
#                           tfr_raw[is.na(tfr_raw)] <- "NA.my";
#                           return(as.factor(tfr_raw)) }
#     , args=c("raw"))
#     mapfn=function(PTS, oppPTS) { return(PTS - oppPTS) }
#     , args=c("PTS", "oppPTS"))

# # If glb_allobs_df is not sorted in the desired manner
#     mapfn=function(Week) { return(coredata(lag(zoo(orderBy(~Week, glb_allobs_df)$ILI), -2, na.pad=TRUE))) }
#     mapfn=function(ILI) { return(coredata(lag(zoo(ILI), -2, na.pad=TRUE))) }
#     mapfn=function(ILI.2.lag) { return(log(ILI.2.lag)) }

# glb_derive_lst[["<txt_var>.niso8859.log"]] <- list(
#     mapfn=function(<txt_var>) { match_lst <- gregexpr("&#[[:digit:]]{3};", <txt_var>)
#                         match_num_vctr <- unlist(lapply(match_lst, 
#                                                         function(elem) length(elem)))
#                         return(log(1 + match_num_vctr)) }
#     , args=c("<txt_var>"))

#     mapfn=function(raw) { mod_raw <- raw;
#         mod_raw <- gsub("&#[[:digit:]]{3};", " ", mod_raw);
#         # Modifications for this exercise only
#         mod_raw <- gsub("\\bgoodIn ", "good In", mod_raw);
#                           return(mod_raw)

#         # Create user-specified pattern vectors 
# #sum(mycount_pattern_occ("Metropolitan Diary:", glb_allobs_df$Abstract) > 0)
#         if (txt_var %in% c("Snippet", "Abstract")) {
#             txt_X_df[, paste0(txt_var_pfx, ".P.metropolitan.diary.colon")] <-
#                 as.integer(0 + mycount_pattern_occ("Metropolitan Diary:", 
#                                                    glb_allobs_df[, txt_var]))
#summary(glb_allobs_df[ ,grep("P.on.this.day", names(glb_allobs_df), value=TRUE)])

# glb_derive_lst[["<var1>"]] <- glb_derive_lst[["<var2>"]]

glb_derive_vars <- names(glb_derive_lst)
# tst <- "PropR.fctr"; args_lst <- NULL; for (arg in glb_derive_lst[[tst]]$args) args_lst[[arg]] <- glb_allobs_df[, arg]; print(head(args_lst[[arg]])); print(head(drv_vals <- do.call(glb_derive_lst[[tst]]$mapfn, args_lst))); 
# print(which_ix <- which(args_lst[[arg]] == 0.75)); print(drv_vals[which_ix]); 

glb_date_vars <- NULL # or c("<date_var>")
glb_date_fmts <- list(); #glb_date_fmts[["<date_var>"]] <- "%m/%e/%y"
glb_date_tzs <- list();  #glb_date_tzs[["<date_var>"]] <- "America/New_York"
#grep("America/New", OlsonNames(), value=TRUE)

glb_txt_vars <- NULL # or c("<txt_var1>", "<txt_var2>")   
#Sys.setlocale("LC_ALL", "C") # For english

glb_append_stop_words <- list()
# Remember to use unstemmed words
#orderBy(~ -cor.y.abs, subset(glb_feats_df, grepl("[HSA]\\.T\\.", id) & !is.na(cor.high.X)))
#dsp_obs(Headline.contains="polit")
#subset(glb_allobs_df, H.T.compani > 0)[, c("UniqueID", "Headline", "H.T.compani")]
# glb_append_stop_words[["<txt_var1>"]] <- c(NULL
# #                             ,"<word1>" # <reason1>
#                             )
#subset(glb_allobs_df, S.T.newyorktim > 0)[, c("UniqueID", "Snippet", "S.T.newyorktim")]
#glb_txt_lst[["Snippet"]][which(glb_allobs_df$UniqueID %in% c(8394, 8317, 8339, 8350, 8307))]

glb_important_terms <- list()
# Remember to use stemmed terms 

glb_sprs_thresholds <- NULL # or c(0.988, 0.970, 0.970) # Generates 29, 22, 22 terms
# Properties:
#   numrows(glb_feats_df) << numrows(glb_fitobs_df)
#   Select terms that appear in at least 0.2 * O(FP/FN(glb_OOBobs_df))
#       numrows(glb_OOBobs_df) = 1.1 * numrows(glb_newobs_df)
names(glb_sprs_thresholds) <- glb_txt_vars

# User-specified exclusions  
glb_exclude_vars_as_features <- c("state", "crime") 
if (glb_rsp_var_raw != glb_rsp_var)
    glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, 
                                            glb_rsp_var_raw)

# List feats that shd be excluded due to known causation by prediction variable
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, 
                                      c(NULL)) # or c("<col_name>")

glb_impute_na_data <- FALSE # or TRUE
glb_mice_complete.seed <- 144 # or any integer

glb_cluster <- FALSE # or TRUE

glb_interaction_only_features <- NULL # or ???

glb_models_lst <- list(); glb_models_df <- data.frame()
# Regression
if (glb_is_regression)
    glb_models_method_vctr <- c("lm", "glm", "bayesglm", "rpart", "rf") else
# Classification
    if (glb_is_binomial)
        glb_models_method_vctr <- c("glm", "bayesglm", "rpart", "rf") else  
        glb_models_method_vctr <- c("rpart", "rf")

# Baseline prediction model feature(s)
glb_Baseline_mdl_var <- NULL # or c("<col_name>")

glb_model_metric_terms <- NULL # or matrix(c(
#                               0,1,2,3,4,
#                               2,0,1,2,3,
#                               4,2,0,1,2,
#                               6,4,2,0,1,
#                               8,6,4,2,0
#                           ), byrow=TRUE, nrow=5)
glb_model_metric <- NULL # or "<metric_name>"
glb_model_metric_maximize <- NULL # or FALSE (TRUE is not the default for both classification & regression) 
glb_model_metric_smmry <- NULL # or function(data, lev=NULL, model=NULL) {
#     confusion_mtrx <- t(as.matrix(confusionMatrix(data$pred, data$obs)))
#     #print(confusion_mtrx)
#     #print(confusion_mtrx * glb_model_metric_terms)
#     metric <- sum(confusion_mtrx * glb_model_metric_terms) / nrow(data)
#     names(metric) <- glb_model_metric
#     return(metric)
# }

glb_tune_models_df <- 
   rbind(
    #data.frame(parameter="cp", min=0.00005, max=0.00005, by=0.000005),
                            #seq(from=0.01,  to=0.01, by=0.01)
    #data.frame(parameter="mtry",  min=080, max=100, by=10),
    #data.frame(parameter="mtry",  min=08, max=10, by=1),    
    data.frame(parameter="dummy", min=2, max=4, by=1)
        ) 
# or NULL
glb_n_cv_folds <- 3 # or NULL

glb_clf_proba_threshold <- NULL # 0.5

# Model selection criteria
if (glb_is_regression)
    glb_model_evl_criteria <- c("min.RMSE.OOB", "max.R.sq.OOB", "max.Adj.R.sq.fit")
if (glb_is_classification) {
    if (glb_is_binomial)
        glb_model_evl_criteria <- 
            c("max.Accuracy.OOB", "max.auc.OOB", "max.Kappa.OOB", "min.aic.fit") else
        glb_model_evl_criteria <- c("max.Accuracy.OOB", "max.Kappa.OOB")
}

glb_sel_mdl_id <- NULL # or "<model_id_prefix>.<model_method>"
glb_fin_mdl_id <- glb_sel_mdl_id # or "Final"

# Depict process
glb_analytics_pn <- petrinet(name="glb_analytics_pn",
                        trans_df=data.frame(id=1:6,
    name=c("data.training.all","data.new",
           "model.selected","model.final",
           "data.training.all.prediction","data.new.prediction"),
    x=c(   -5,-5,-15,-25,-25,-35),
    y=c(   -5, 5,  0,  0, -5,  5)
                        ),
                        places_df=data.frame(id=1:4,
    name=c("bgn","fit.data.training.all","predict.data.new","end"),
    x=c(   -0,   -20,                    -30,               -40),
    y=c(    0,     0,                      0,                 0),
    M0=c(   3,     0,                      0,                 0)
                        ),
                        arcs_df=data.frame(
    begin=c("bgn","bgn","bgn",        
            "data.training.all","model.selected","fit.data.training.all",
            "fit.data.training.all","model.final",    
            "data.new","predict.data.new",
            "data.training.all.prediction","data.new.prediction"),
    end  =c("data.training.all","data.new","model.selected",
            "fit.data.training.all","fit.data.training.all","model.final",
            "data.training.all.prediction","predict.data.new",
            "predict.data.new","data.new.prediction",
            "end","end")
                        ))
#print(ggplot.petrinet(glb_analytics_pn))
print(ggplot.petrinet(glb_analytics_pn) + coord_flip())
## Loading required package: grid

glb_analytics_avl_objs <- NULL

glb_chunks_df <- myadd_chunk(NULL, "import.data")
##         label step_major step_minor    bgn end elapsed
## 1 import.data          1          0 12.683  NA      NA

Step 1.0: import data

chunk option: eval=

#glb_chunks_df <- myadd_chunk(NULL, "import.data")

glb_trnobs_df <- myimport_data(url=glb_trnng_url, comment="glb_trnobs_df", 
                                force_header=TRUE)
## [1] "Reading file ./data/parole.csv..."
## [1] "dimensions of data in ./data/parole.csv: 675 rows x 9 cols"
##   male race  age state time.served max.sentence multiple.offenses crime
## 1    1    1 33.2     1         5.5           18                 0     4
## 2    0    1 39.7     1         5.4           12                 0     3
## 3    1    2 29.5     1         5.6           12                 0     3
## 4    1    1 22.4     1         5.7           18                 0     1
## 5    1    2 21.6     1         5.4           12                 0     1
## 6    1    2 46.7     1         6.0           18                 0     4
##   violator
## 1        0
## 2        0
## 3        0
## 4        0
## 5        0
## 6        0
##     male race  age state time.served max.sentence multiple.offenses crime
## 24     1    1 38.9     1         5.2           16                 0     3
## 103    0    1 35.0     2         5.7           12                 0     3
## 344    1    1 44.9     4         5.3           12                 1     1
## 491    1    1 20.6     4         4.3           13                 1     2
## 493    1    2 34.9     4         5.1           13                 1     2
## 667    1    2 25.4     4         3.4           14                 1     1
##     violator
## 24         0
## 103        0
## 344        0
## 491        0
## 493        0
## 667        0
##     male race  age state time.served max.sentence multiple.offenses crime
## 670    0    2 42.0     4         3.3           13                 1     1
## 671    1    1 47.1     4         4.2           16                 1     1
## 672    0    1 47.5     1         5.2           16                 0     3
## 673    1    1 45.4     1         5.7           12                 0     3
## 674    1    1 38.4     1         1.8           18                 0     1
## 675    1    1 47.8     1         6.0           12                 0     4
##     violator
## 670        0
## 671        0
## 672        0
## 673        0
## 674        0
## 675        0
## 'data.frame':    675 obs. of  9 variables:
##  $ male             : int  1 0 1 1 1 1 1 0 0 1 ...
##  $ race             : int  1 1 2 1 2 2 1 1 1 2 ...
##  $ age              : num  33.2 39.7 29.5 22.4 21.6 46.7 31 24.6 32.6 29.1 ...
##  $ state            : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ time.served      : num  5.5 5.4 5.6 5.7 5.4 6 6 4.8 4.5 4.7 ...
##  $ max.sentence     : int  18 12 12 18 12 18 18 12 13 12 ...
##  $ multiple.offenses: int  0 0 0 0 0 0 0 0 0 0 ...
##  $ crime            : int  4 3 3 1 1 4 3 1 3 2 ...
##  $ violator         : int  0 0 0 0 0 0 0 0 0 0 ...
##  - attr(*, "comment")= chr "glb_trnobs_df"
## NULL
# glb_trnobs_df <- read.delim("data/hygiene.txt", header=TRUE, fill=TRUE, sep="\t",
#                             fileEncoding='iso-8859-1')
# glb_trnobs_df <- read.table("data/hygiene.dat.labels", col.names=c("dirty"),
#                             na.strings="[none]")
# glb_trnobs_df$review <- readLines("data/hygiene.dat", n =-1)
# comment(glb_trnobs_df) <- "glb_trnobs_df"                                

# glb_trnobs_df <- data.frame()
# for (symbol in c("Boeing", "CocaCola", "GE", "IBM", "ProcterGamble")) {
#     sym_trnobs_df <- 
#         myimport_data(url=gsub("IBM", symbol, glb_trnng_url), comment="glb_trnobs_df", 
#                                     force_header=TRUE)
#     sym_trnobs_df$Symbol <- symbol
#     glb_trnobs_df <- myrbind_df(glb_trnobs_df, sym_trnobs_df)
# }
                                
# glb_trnobs_df <- 
#     glb_trnobs_df %>% dplyr::filter(Year >= 1999)
                                
if (glb_is_separate_newobs_dataset) {
    glb_newobs_df <- myimport_data(url=glb_newdt_url, comment="glb_newobs_df", 
                                   force_header=TRUE)
    
    # To make plots / stats / checks easier in chunk:inspectORexplore.data
    glb_allobs_df <- myrbind_df(glb_trnobs_df, glb_newobs_df); 
    comment(glb_allobs_df) <- "glb_allobs_df"
} else {
    glb_allobs_df <- glb_trnobs_df; comment(glb_allobs_df) <- "glb_allobs_df"
    if (!glb_split_entity_newobs_datasets) {
        stop("Not implemented yet") 
        glb_newobs_df <- glb_trnobs_df[sample(1:nrow(glb_trnobs_df),
                                          max(2, nrow(glb_trnobs_df) / 1000)),]                    
    } else      if (glb_split_newdata_method == "condition") {
            glb_newobs_df <- do.call("subset", 
                list(glb_trnobs_df, parse(text=glb_split_newdata_condition)))
            glb_trnobs_df <- do.call("subset", 
                list(glb_trnobs_df, parse(text=paste0("!(", 
                                                      glb_split_newdata_condition,
                                                      ")"))))
        } else if (glb_split_newdata_method == "sample") {
                require(caTools)
                
                set.seed(glb_split_sample.seed)
                split <- sample.split(glb_trnobs_df[, glb_rsp_var_raw], 
                                      SplitRatio=(1-glb_split_newdata_size_ratio))
                glb_newobs_df <- glb_trnobs_df[!split, ] 
                glb_trnobs_df <- glb_trnobs_df[split ,]
        } else if (glb_split_newdata_method == "copy") {  
            glb_trnobs_df <- glb_allobs_df
            comment(glb_trnobs_df) <- "glb_trnobs_df"
            glb_newobs_df <- glb_allobs_df
            comment(glb_newobs_df) <- "glb_newobs_df"
        } else stop("glb_split_newdata_method should be %in% c('condition', 'sample', 'copy')")   

    comment(glb_newobs_df) <- "glb_newobs_df"
    myprint_df(glb_newobs_df)
    str(glb_newobs_df)

    if (glb_split_entity_newobs_datasets) {
        myprint_df(glb_trnobs_df)
        str(glb_trnobs_df)        
    }
}         
## Loading required package: caTools
##    male race  age state time.served max.sentence multiple.offenses crime
## 2     0    1 39.7     1         5.4           12                 0     3
## 3     1    2 29.5     1         5.6           12                 0     3
## 8     0    1 24.6     1         4.8           12                 0     1
## 10    1    2 29.1     1         4.7           12                 0     2
## 19    1    2 24.5     1         6.0           16                 0     3
## 27    1    1 32.8     1         5.9           16                 0     3
##    violator
## 2         0
## 3         0
## 8         0
## 10        0
## 19        0
## 27        0
##     male race  age state time.served max.sentence multiple.offenses crime
## 126    1    1 40.4     2         4.2           12                 0     1
## 130    1    2 18.7     2         5.2           12                 0     1
## 176    1    1 19.5     2         5.3           12                 0     1
## 254    1    2 21.6     3         4.0            8                 1     3
## 282    0    1 51.8     1         6.0           12                 0     1
## 395    0    2 46.0     4         4.5           15                 1     1
##     violator
## 126        0
## 130        1
## 176        0
## 254        1
## 282        0
## 395        0
##     male race  age state time.served max.sentence multiple.offenses crime
## 661    1    1 22.1     4         3.8           14                 1     1
## 665    1    1 56.5     4         5.8           18                 0     1
## 669    1    1 39.0     4         3.9           14                 1     2
## 672    0    1 47.5     1         5.2           16                 0     3
## 673    1    1 45.4     1         5.7           12                 0     3
## 674    1    1 38.4     1         1.8           18                 0     1
##     violator
## 661        0
## 665        0
## 669        0
## 672        0
## 673        0
## 674        0
## 'data.frame':    202 obs. of  9 variables:
##  $ male             : int  0 1 0 1 1 1 1 1 1 1 ...
##  $ race             : int  1 2 1 2 2 1 1 2 1 1 ...
##  $ age              : num  39.7 29.5 24.6 29.1 24.5 32.8 36.7 36.5 33.5 37.3 ...
##  $ state            : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ time.served      : num  5.4 5.6 4.8 4.7 6 5.9 0.9 3.9 4.2 4.6 ...
##  $ max.sentence     : int  12 12 12 12 16 16 16 12 12 12 ...
##  $ multiple.offenses: int  0 0 0 0 0 0 0 1 1 1 ...
##  $ crime            : int  3 3 1 2 3 3 3 4 1 1 ...
##  $ violator         : int  0 0 0 0 0 0 0 1 1 1 ...
##  - attr(*, "comment")= chr "glb_newobs_df"
##   male race  age state time.served max.sentence multiple.offenses crime
## 1    1    1 33.2     1         5.5           18                 0     4
## 4    1    1 22.4     1         5.7           18                 0     1
## 5    1    2 21.6     1         5.4           12                 0     1
## 6    1    2 46.7     1         6.0           18                 0     4
## 7    1    1 31.0     1         6.0           18                 0     3
## 9    0    1 32.6     1         4.5           13                 0     3
##   violator
## 1        0
## 4        0
## 5        0
## 6        0
## 7        0
## 9        0
##     male race  age state time.served max.sentence multiple.offenses crime
## 23     1    1 41.9     1         5.1           16                 0     3
## 165    1    1 32.7     2         5.1           12                 1     1
## 248    1    2 28.4     3         2.2           12                 1     1
## 503    1    2 49.0     4         4.9           16                 0     1
## 565    1    1 39.7     4         5.6           18                 1     1
## 616    1    2 43.7     4         5.6           18                 1     4
##     violator
## 23         0
## 165        0
## 248        1
## 503        0
## 565        1
## 616        0
##     male race  age state time.served max.sentence multiple.offenses crime
## 666    1    2 36.4     4         2.9           12                 1     2
## 667    1    2 25.4     4         3.4           14                 1     1
## 668    1    2 28.2     4         6.0           18                 1     4
## 670    0    2 42.0     4         3.3           13                 1     1
## 671    1    1 47.1     4         4.2           16                 1     1
## 675    1    1 47.8     1         6.0           12                 0     4
##     violator
## 666        0
## 667        0
## 668        0
## 670        0
## 671        0
## 675        0
## 'data.frame':    473 obs. of  9 variables:
##  $ male             : int  1 1 1 1 1 0 0 1 1 1 ...
##  $ race             : int  1 1 2 2 1 1 2 1 1 1 ...
##  $ age              : num  33.2 22.4 21.6 46.7 31 32.6 28.4 20.5 30.1 37.8 ...
##  $ state            : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ time.served      : num  5.5 5.7 5.4 6 6 4.5 4.5 5.9 5.3 5.3 ...
##  $ max.sentence     : int  18 18 12 18 18 13 12 12 16 8 ...
##  $ multiple.offenses: int  0 0 0 0 0 0 1 0 0 0 ...
##  $ crime            : int  4 1 1 4 3 3 1 1 3 3 ...
##  $ violator         : int  0 0 0 0 0 0 0 0 0 0 ...
##  - attr(*, "comment")= chr "glb_trnobs_df"
if ((num_nas <- sum(is.na(glb_trnobs_df[, glb_rsp_var_raw]))) > 0)
    stop("glb_trnobs_df$", glb_rsp_var_raw, " contains NAs for ", num_nas, " obs")

if (nrow(glb_trnobs_df) == nrow(glb_allobs_df))
    warning("glb_trnobs_df same as glb_allobs_df")
if (nrow(glb_newobs_df) == nrow(glb_allobs_df))
    warning("glb_newobs_df same as glb_allobs_df")

if (length(glb_drop_vars) > 0) {
    warning("dropping vars: ", paste0(glb_drop_vars, collapse=", "))
    glb_allobs_df <- glb_allobs_df[, setdiff(names(glb_allobs_df), glb_drop_vars)]
    glb_trnobs_df <- glb_trnobs_df[, setdiff(names(glb_trnobs_df), glb_drop_vars)]    
    glb_newobs_df <- glb_newobs_df[, setdiff(names(glb_newobs_df), glb_drop_vars)]    
}

#stop(here"); sav_allobs_df <- glb_allobs_df # glb_allobs_df <- sav_allobs_df
# Combine trnent & newobs into glb_allobs_df for easier manipulation
glb_trnobs_df$.src <- "Train"; glb_newobs_df$.src <- "Test"; 
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, ".src")
glb_allobs_df <- myrbind_df(glb_trnobs_df, glb_newobs_df)
comment(glb_allobs_df) <- "glb_allobs_df"

# Check for duplicates in glb_id_var
if (length(glb_id_var) == 0) {
    warning("using .rownames as identifiers for observations")
    glb_allobs_df$.rownames <- rownames(glb_allobs_df)
    glb_trnobs_df$.rownames <- rownames(subset(glb_allobs_df, .src == "Train"))
    glb_newobs_df$.rownames <- rownames(subset(glb_allobs_df, .src == "Test"))    
    glb_id_var <- ".rownames"
}
## Warning: using .rownames as identifiers for observations
if (sum(duplicated(glb_allobs_df[, glb_id_var, FALSE])) > 0)
    stop(glb_id_var, " duplicated in glb_allobs_df")
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_id_var)

glb_allobs_df <- orderBy(reformulate(glb_id_var), glb_allobs_df)
glb_trnobs_df <- glb_newobs_df <- NULL

glb_chunks_df <- myadd_chunk(glb_chunks_df, "inspect.data", major.inc=TRUE)
##          label step_major step_minor    bgn   end elapsed
## 1  import.data          1          0 12.683 13.14   0.457
## 2 inspect.data          2          0 13.140    NA      NA

Step 2.0: inspect data

#print(str(glb_allobs_df))
#View(glb_allobs_df)

dsp_class_dstrb <- function(var) {
    xtab_df <- mycreate_xtab_df(glb_allobs_df, c(".src", var))
    rownames(xtab_df) <- xtab_df$.src
    xtab_df <- subset(xtab_df, select=-.src)
    print(xtab_df)
    print(xtab_df / rowSums(xtab_df, na.rm=TRUE))    
}    

# Performed repeatedly in other chunks
glb_chk_data <- function() {
    # Histogram of predictor in glb_trnobs_df & glb_newobs_df
    print(myplot_histogram(glb_allobs_df, glb_rsp_var_raw) + facet_wrap(~ .src))
    
    if (glb_is_classification) 
        dsp_class_dstrb(var=ifelse(glb_rsp_var %in% names(glb_allobs_df), 
                                   glb_rsp_var, glb_rsp_var_raw))
    mycheck_problem_data(glb_allobs_df)
}
glb_chk_data()
## stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
## stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
## Loading required package: reshape2

##       violator.0 violator.1
## Test         179         23
## Train        418         55
##       violator.0 violator.1
## Test   0.8861386  0.1138614
## Train  0.8837209  0.1162791
## [1] "numeric data missing in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ 0s in glb_allobs_df: "
##              male       time.served multiple.offenses          violator 
##               130                 1               313               597 
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## .rownames 
##         0
# Create new features that help diagnostics
if (!is.null(glb_map_rsp_raw_to_var)) {
    glb_allobs_df[, glb_rsp_var] <- 
        glb_map_rsp_raw_to_var(glb_allobs_df[, glb_rsp_var_raw])
    mycheck_map_results(mapd_df=glb_allobs_df, 
                        from_col_name=glb_rsp_var_raw, to_col_name=glb_rsp_var)
        
    if (glb_is_classification) dsp_class_dstrb(glb_rsp_var)
}
## Loading required package: sqldf
## Loading required package: gsubfn
## Loading required package: proto
## Loading required package: RSQLite
## Loading required package: DBI
## Loading required package: tcltk
##   violator violator.fctr  .n
## 1        0             N 597
## 2        1             Y  78

##       violator.fctr.N violator.fctr.Y
## Test              179              23
## Train             418              55
##       violator.fctr.N violator.fctr.Y
## Test        0.8861386       0.1138614
## Train       0.8837209       0.1162791
# check distribution of all numeric data
dsp_numeric_feats_dstrb <- function(feats_vctr) {
    for (feat in feats_vctr) {
        print(sprintf("feat: %s", feat))
        if (glb_is_regression)
            gp <- myplot_scatter(df=glb_allobs_df, ycol_name=glb_rsp_var, xcol_name=feat,
                                 smooth=TRUE)
        if (glb_is_classification)
            gp <- myplot_box(df=glb_allobs_df, ycol_names=feat, xcol_name=glb_rsp_var)
        if (inherits(glb_allobs_df[, feat], "factor"))
            gp <- gp + facet_wrap(reformulate(feat))
        print(gp)
    }
}
# dsp_numeric_vars_dstrb(setdiff(names(glb_allobs_df), 
#                                 union(myfind_chr_cols_df(glb_allobs_df), 
#                                       c(glb_rsp_var_raw, glb_rsp_var))))                                      

add_new_diag_feats <- function(obs_df, ref_df=glb_allobs_df) {
    require(plyr)
    
    obs_df <- mutate(obs_df,
#         <col_name>.NA=is.na(<col_name>),

#         <col_name>.fctr=factor(<col_name>, 
#                     as.factor(union(obs_df$<col_name>, obs_twin_df$<col_name>))), 
#         <col_name>.fctr=relevel(factor(<col_name>, 
#                     as.factor(union(obs_df$<col_name>, obs_twin_df$<col_name>))),
#                                   "<ref_val>"), 
#         <col2_name>.fctr=relevel(factor(ifelse(<col1_name> == <val>, "<oth_val>", "<ref_val>")), 
#                               as.factor(c("R", "<ref_val>")),
#                               ref="<ref_val>"),

          # This doesn't work - use sapply instead
#         <col_name>.fctr_num=grep(<col_name>, levels(<col_name>.fctr)), 
#         
#         Date.my=as.Date(strptime(Date, "%m/%d/%y %H:%M")),
#         Year=year(Date.my),
#         Month=months(Date.my),
#         Weekday=weekdays(Date.my)

#         <col_name>=<table>[as.character(<col2_name>)],
#         <col_name>=as.numeric(<col2_name>),

#         <col_name> = trunc(<col2_name> / 100),

        .rnorm = rnorm(n=nrow(obs_df))
                        )

    # If levels of a factor are different across obs_df & glb_newobs_df; predict.glm fails  
    # Transformations not handled by mutate
#     obs_df$<col_name>.fctr.num <- sapply(1:nrow(obs_df), 
#         function(row_ix) grep(obs_df[row_ix, "<col_name>"],
#                               levels(obs_df[row_ix, "<col_name>.fctr"])))
    
    #print(summary(obs_df))
    #print(sapply(names(obs_df), function(col) sum(is.na(obs_df[, col]))))
    return(obs_df)
}
glb_allobs_df <- add_new_diag_feats(glb_allobs_df)
## Loading required package: plyr
require(dplyr)
## Loading required package: dplyr
## 
## Attaching package: 'dplyr'
## 
## The following objects are masked from 'package:plyr':
## 
##     arrange, count, desc, failwith, id, mutate, rename, summarise,
##     summarize
## 
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## 
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
#stop(here"); sav_allobs_df <- glb_allobs_df # glb_allobs_df <- sav_allobs_df
# Merge some <descriptor>
# glb_allobs_df$<descriptor>.my <- glb_allobs_df$<descriptor>
# glb_allobs_df[grepl("\\bAIRPORT\\b", glb_allobs_df$<descriptor>.my),
#               "<descriptor>.my"] <- "AIRPORT"
# glb_allobs_df$<descriptor>.my <-
#     plyr::revalue(glb_allobs_df$<descriptor>.my, c(
#         "ABANDONED BUILDING" = "OTHER",
#         "##"                      = "##"
#     ))
# print(<descriptor>_freq_df <- mycreate_sqlxtab_df(glb_allobs_df, c("<descriptor>.my")))
# # print(dplyr::filter(<descriptor>_freq_df, grepl("(MEDICAL|DENTAL|OFFICE)", <descriptor>.my)))
# # print(dplyr::filter(dplyr::select(glb_allobs_df, -<var.zoo>), 
# #                     grepl("STORE", <descriptor>.my)))
# glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, "<descriptor>")

# Check distributions of newly transformed / extracted vars
#   Enhancement: remove vars that were displayed ealier
dsp_numeric_feats_dstrb(feats_vctr=setdiff(names(glb_allobs_df), 
        c(myfind_chr_cols_df(glb_allobs_df), glb_rsp_var_raw, glb_rsp_var, 
          glb_exclude_vars_as_features)))
## [1] "feat: male"

## [1] "feat: race"

## [1] "feat: age"

## [1] "feat: time.served"

## [1] "feat: max.sentence"

## [1] "feat: multiple.offenses"

## [1] "feat: .rnorm"

#   Convert factors to dummy variables
#   Build splines   require(splines); bsBasis <- bs(training$age, df=3)

#pairs(subset(glb_trnobs_df, select=-c(col_symbol)))
# Check for glb_newobs_df & glb_trnobs_df features range mismatches

# Other diagnostics:
# print(subset(glb_trnobs_df, <col1_name> == max(glb_trnobs_df$<col1_name>, na.rm=TRUE) & 
#                         <col2_name> <= mean(glb_trnobs_df$<col1_name>, na.rm=TRUE)))

# print(glb_trnobs_df[which.max(glb_trnobs_df$<col_name>),])

# print(<col_name>_freq_glb_trnobs_df <- mycreate_tbl_df(glb_trnobs_df, "<col_name>"))
# print(which.min(table(glb_trnobs_df$<col_name>)))
# print(which.max(table(glb_trnobs_df$<col_name>)))
# print(which.max(table(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>)[, 2]))
# print(table(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>))
# print(table(is.na(glb_trnobs_df$<col1_name>), glb_trnobs_df$<col2_name>))
# print(table(sign(glb_trnobs_df$<col1_name>), glb_trnobs_df$<col2_name>))
# print(mycreate_xtab_df(glb_trnobs_df, <col1_name>))
# print(mycreate_xtab_df(glb_trnobs_df, c(<col1_name>, <col2_name>)))
# print(<col1_name>_<col2_name>_xtab_glb_trnobs_df <- 
#   mycreate_xtab_df(glb_trnobs_df, c("<col1_name>", "<col2_name>")))
# <col1_name>_<col2_name>_xtab_glb_trnobs_df[is.na(<col1_name>_<col2_name>_xtab_glb_trnobs_df)] <- 0
# print(<col1_name>_<col2_name>_xtab_glb_trnobs_df <- 
#   mutate(<col1_name>_<col2_name>_xtab_glb_trnobs_df, 
#             <col3_name>=(<col1_name> * 1.0) / (<col1_name> + <col2_name>))) 
# print(mycreate_sqlxtab_df(glb_allobs_df, c("<col1_name>", "<col2_name>")))

# print(<col2_name>_min_entity_arr <- 
#    sort(tapply(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>, min, na.rm=TRUE)))
# print(<col1_name>_na_by_<col2_name>_arr <- 
#    sort(tapply(glb_trnobs_df$<col1_name>.NA, glb_trnobs_df$<col2_name>, mean, na.rm=TRUE)))

# Other plots:
# print(myplot_box(df=glb_trnobs_df, ycol_names="<col1_name>"))
# print(myplot_box(df=glb_trnobs_df, ycol_names="<col1_name>", xcol_name="<col2_name>"))
# print(myplot_line(subset(glb_trnobs_df, Symbol %in% c("CocaCola", "ProcterGamble")), 
#                   "Date.POSIX", "StockPrice", facet_row_colnames="Symbol") + 
#     geom_vline(xintercept=as.numeric(as.POSIXlt("2003-03-01"))) +
#     geom_vline(xintercept=as.numeric(as.POSIXlt("1983-01-01")))        
#         )
# print(myplot_line(subset(glb_trnobs_df, Date.POSIX > as.POSIXct("2004-01-01")), 
#                   "Date.POSIX", "StockPrice") +
#     geom_line(aes(color=Symbol)) + 
#     coord_cartesian(xlim=c(as.POSIXct("1990-01-01"),
#                            as.POSIXct("2000-01-01"))) +     
#     coord_cartesian(ylim=c(0, 250)) +     
#     geom_vline(xintercept=as.numeric(as.POSIXlt("1997-09-01"))) +
#     geom_vline(xintercept=as.numeric(as.POSIXlt("1997-11-01")))        
#         )
# print(myplot_scatter(glb_allobs_df, "<col1_name>", "<col2_name>", smooth=TRUE))
# print(myplot_scatter(glb_allobs_df, "<col1_name>", "<col2_name>", colorcol_name="<Pred.fctr>") + 
#         geom_point(data=subset(glb_allobs_df, <condition>), 
#                     mapping=aes(x=<x_var>, y=<y_var>), color="red", shape=4, size=5) +
#         geom_vline(xintercept=84))

glb_chunks_df <- myadd_chunk(glb_chunks_df, "scrub.data", major.inc=FALSE)
##          label step_major step_minor   bgn    end elapsed
## 2 inspect.data          2          0 13.14 20.289   7.149
## 3   scrub.data          2          1 20.29     NA      NA

Step 2.1: scrub data

mycheck_problem_data(glb_allobs_df)
## [1] "numeric data missing in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ 0s in glb_allobs_df: "
##              male       time.served multiple.offenses          violator 
##               130                 1               313               597 
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## .rownames 
##         0
dsp_catgs <- function() {
    print("NewsDesk:")
    print(table(glb_allobs_df$NewsDesk))
    print("SectionName:")    
    print(table(glb_allobs_df$SectionName))
    print("SubsectionName:")        
    print(table(glb_allobs_df$SubsectionName))
}

# sel_obs <- function(Popular=NULL, 
#                     NewsDesk=NULL, SectionName=NULL, SubsectionName=NULL,
#         Headline.contains=NULL, Snippet.contains=NULL, Abstract.contains=NULL,
#         Headline.pfx=NULL, NewsDesk.nb=NULL, .clusterid=NULL, myCategory=NULL,
#         perl=FALSE) {
sel_obs <- function(vars_lst) {
    tmp_df <- glb_allobs_df
    # Does not work for Popular == NAs ???
    if (!is.null(Popular)) {
        if (is.na(Popular))
            tmp_df <- tmp_df[is.na(tmp_df$Popular), ] else   
            tmp_df <- tmp_df[tmp_df$Popular == Popular, ]    
    }    
    if (!is.null(NewsDesk)) 
        tmp_df <- tmp_df[tmp_df$NewsDesk == NewsDesk, ]
    if (!is.null(SectionName)) 
        tmp_df <- tmp_df[tmp_df$SectionName == SectionName, ]
    if (!is.null(SubsectionName)) 
        tmp_df <- tmp_df[tmp_df$SubsectionName == SubsectionName, ]
    if (!is.null(Headline.contains))
        tmp_df <- 
            tmp_df[grep(Headline.contains, tmp_df$Headline, perl=perl), ]
    if (!is.null(Snippet.contains))
        tmp_df <- 
            tmp_df[grep(Snippet.contains, tmp_df$Snippet, perl=perl), ]
    if (!is.null(Abstract.contains))
        tmp_df <- 
            tmp_df[grep(Abstract.contains, tmp_df$Abstract, perl=perl), ]
    if (!is.null(Headline.pfx)) {
        if (length(grep("Headline.pfx", names(tmp_df), fixed=TRUE, value=TRUE))
            > 0) tmp_df <- 
                tmp_df[tmp_df$Headline.pfx == Headline.pfx, ] else
        warning("glb_allobs_df does not contain Headline.pfx; ignoring that filter")                    
    }    
    if (!is.null(NewsDesk.nb)) {
        if (any(grepl("NewsDesk.nb", names(tmp_df), fixed=TRUE)) > 0) 
            tmp_df <- 
                tmp_df[tmp_df$NewsDesk.nb == NewsDesk.nb, ] else
        warning("glb_allobs_df does not contain NewsDesk.nb; ignoring that filter")                    
    }    
    if (!is.null(.clusterid)) {
        if (any(grepl(".clusterid", names(tmp_df), fixed=TRUE)) > 0) 
            tmp_df <- 
                tmp_df[tmp_df$clusterid == clusterid, ] else
        warning("glb_allobs_df does not contain clusterid; ignoring that filter")                       }
    if (!is.null(myCategory)) {    
        if (!(myCategory %in% names(glb_allobs_df)))
            tmp_df <-
                tmp_df[tmp_df$myCategory == myCategory, ] else
        warning("glb_allobs_df does not contain myCategory; ignoring that filter")                    
    }    
    
    return(glb_allobs_df$UniqueID %in% tmp_df$UniqueID)
}

dsp_obs <- function(..., cols=c(NULL), all=FALSE) {
    tmp_df <- glb_allobs_df[sel_obs(...), 
                            union(c("UniqueID", "Popular", "myCategory", "Headline"), cols), FALSE]
    if(all) { print(tmp_df) } else { myprint_df(tmp_df) }
}
#dsp_obs(Popular=1, NewsDesk="", SectionName="", Headline.contains="Boehner")
# dsp_obs(Popular=1, NewsDesk="", SectionName="")
# dsp_obs(Popular=NA, NewsDesk="", SectionName="")

dsp_tbl <- function(...) {
    tmp_entity_df <- glb_allobs_df[sel_obs(...), ]
    tmp_tbl <- table(tmp_entity_df$NewsDesk, 
                     tmp_entity_df$SectionName,
                     tmp_entity_df$SubsectionName, 
                     tmp_entity_df$Popular, useNA="ifany")
    #print(names(tmp_tbl))
    #print(dimnames(tmp_tbl))
    print(tmp_tbl)
}

dsp_hdlxtab <- function(str) 
    print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains=str), ],
                           c("Headline.pfx", "Headline", glb_rsp_var)))
#dsp_hdlxtab("(1914)|(1939)")

dsp_catxtab <- function(str) 
    print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains=str), ],
        c("Headline.pfx", "NewsDesk", "SectionName", "SubsectionName", glb_rsp_var)))
# dsp_catxtab("1914)|(1939)")
# dsp_catxtab("19(14|39|64):")
# dsp_catxtab("19..:")

# Create myCategory <- NewsDesk#SectionName#SubsectionName
#   Fix some data before merging categories
# glb_allobs_df[sel_obs(Headline.contains="Your Turn:", NewsDesk=""),
#               "NewsDesk"] <- "Styles"
# glb_allobs_df[sel_obs(Headline.contains="School", NewsDesk="", SectionName="U.S.",
#                       SubsectionName=""),
#               "SubsectionName"] <- "Education"
# glb_allobs_df[sel_obs(Headline.contains="Today in Small Business:", NewsDesk="Business"),
#               "SectionName"] <- "Business Day"
# glb_allobs_df[sel_obs(Headline.contains="Today in Small Business:", NewsDesk="Business"),
#               "SubsectionName"] <- "Small Business"
# glb_allobs_df[sel_obs(Headline.contains="Readers Respond:"),
#               "SectionName"] <- "Opinion"
# glb_allobs_df[sel_obs(Headline.contains="Readers Respond:"),
#               "SubsectionName"] <- "Room For Debate"

# glb_allobs_df[sel_obs(NewsDesk="Business", SectionName="", SubsectionName="", Popular=NA),
#               "SubsectionName"] <- "Small Business"
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(7973), 
#     c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
# 
# glb_allobs_df[sel_obs(NewsDesk="Business", SectionName="", SubsectionName=""),
#               "SectionName"] <- "Technology"
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(5076, 5736, 5924, 5911, 6532), 
#     c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
# 
# glb_allobs_df[sel_obs(SectionName="Health"),
#               "NewsDesk"] <- "Science"
# glb_allobs_df[sel_obs(SectionName="Travel"),
#               "NewsDesk"] <- "Travel"
# 
# glb_allobs_df[sel_obs(SubsectionName="Fashion & Style"),
#               "SectionName"] <- ""
# glb_allobs_df[sel_obs(SubsectionName="Fashion & Style"),
#               "SubsectionName"] <- ""
# glb_allobs_df[sel_obs(NewsDesk="Styles", SectionName="", SubsectionName="", Popular=1),
#               "SectionName"] <- "U.S."
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(5486), 
#     c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
# 
# glb_allobs_df$myCategory <- paste(glb_allobs_df$NewsDesk, 
#                                   glb_allobs_df$SectionName,
#                                   glb_allobs_df$SubsectionName,
#                                   sep="#")

# dsp_obs( Headline.contains="Music:"
#         #,NewsDesk=""
#         #,SectionName=""  
#         #,SubsectionName="Fashion & Style"
#         #,Popular=1 #NA
#         ,cols= c("UniqueID", "Headline", "Popular", "myCategory", 
#                 "NewsDesk", "SectionName", "SubsectionName"),
#         all=TRUE)
# dsp_obs( Headline.contains="."
#         ,NewsDesk=""
#         ,SectionName="Opinion"  
#         ,SubsectionName=""
#         #,Popular=1 #NA
#         ,cols= c("UniqueID", "Headline", "Popular", "myCategory", 
#                 "NewsDesk", "SectionName", "SubsectionName"),
#         all=TRUE)
                                        
# Merge some categories
# glb_allobs_df$myCategory <-
#     plyr::revalue(glb_allobs_df$myCategory, c(      
#         "#Business Day#Dealbook"            = "Business#Business Day#Dealbook",
#         "#Business Day#Small Business"      = "Business#Business Day#Small Business",
#         "#Crosswords/Games#"                = "Business#Crosswords/Games#",
#         "Business##"                        = "Business#Technology#",
#         "#Open#"                            = "Business#Technology#",
#         "#Technology#"                      = "Business#Technology#",
#         
#         "#Arts#"                            = "Culture#Arts#",        
#         "Culture##"                         = "Culture#Arts#",        
#         
#         "#World#Asia Pacific"               = "Foreign#World#Asia Pacific",        
#         "Foreign##"                         = "Foreign#World#",    
#         
#         "#N.Y. / Region#"                   = "Metro#N.Y. / Region#",  
#         
#         "#Opinion#"                         = "OpEd#Opinion#",                
#         "OpEd##"                            = "OpEd#Opinion#",        
# 
#         "#Health#"                          = "Science#Health#",
#         "Science##"                         = "Science#Health#",        
#         
#         "Styles##"                          = "Styles##Fashion",                        
#         "Styles#Health#"                    = "Science#Health#",                
#         "Styles#Style#Fashion & Style"      = "Styles##Fashion",        
# 
#         "#Travel#"                          = "Travel#Travel#",                
#         
#         "Magazine#Magazine#"                = "myOther",
#         "National##"                        = "myOther",
#         "National#U.S.#Politics"            = "myOther",        
#         "Sports##"                          = "myOther",
#         "Sports#Sports#"                    = "myOther",
#         "#U.S.#"                            = "myOther",        
#         
# 
# #         "Business##Small Business"        = "Business#Business Day#Small Business",        
# #         
# #         "#Opinion#"                       = "#Opinion#Room For Debate",        
#         "##"                                = "##"
# #         "Business##" = "Business#Business Day#Dealbook",
# #         "Foreign#World#" = "Foreign##",
# #         "#Open#" = "Other",
# #         "#Opinion#The Public Editor" = "OpEd#Opinion#",
# #         "Styles#Health#" = "Styles##",
# #         "Styles#Style#Fashion & Style" = "Styles##",
# #         "#U.S.#" = "#U.S.#Education",
#     ))

# ctgry_xtab_df <- orderBy(reformulate(c("-", ".n")),
#                           mycreate_sqlxtab_df(glb_allobs_df,
#     c("myCategory", "NewsDesk", "SectionName", "SubsectionName", glb_rsp_var)))
# myprint_df(ctgry_xtab_df)
# write.table(ctgry_xtab_df, paste0(glb_out_pfx, "ctgry_xtab.csv"), 
#             row.names=FALSE)

# ctgry_cast_df <- orderBy(~ -Y -NA, dcast(ctgry_xtab_df, 
#                        myCategory + NewsDesk + SectionName + SubsectionName ~ 
#                            Popular.fctr, sum, value.var=".n"))
# myprint_df(ctgry_cast_df)
# write.table(ctgry_cast_df, paste0(glb_out_pfx, "ctgry_cast.csv"), 
#             row.names=FALSE)

# print(ctgry_sum_tbl <- table(glb_allobs_df$myCategory, glb_allobs_df[, glb_rsp_var], 
#                              useNA="ifany"))

dsp_chisq.test <- function(...) {
    sel_df <- glb_allobs_df[sel_obs(...) & 
                            !is.na(glb_allobs_df$Popular), ]
    sel_df$.marker <- 1
    ref_df <- glb_allobs_df[!is.na(glb_allobs_df$Popular), ]
    mrg_df <- merge(ref_df[, c(glb_id_var, "Popular")],
                    sel_df[, c(glb_id_var, ".marker")], all.x=TRUE)
    mrg_df[is.na(mrg_df)] <- 0
    print(mrg_tbl <- table(mrg_df$.marker, mrg_df$Popular))
    print("Rows:Selected; Cols:Popular")
    #print(mrg_tbl)
    print(chisq.test(mrg_tbl))
}
# dsp_chisq.test(Headline.contains="[Ee]bola")
# dsp_chisq.test(Snippet.contains="[Ee]bola")
# dsp_chisq.test(Abstract.contains="[Ee]bola")

# print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains="[Ee]bola"), ], 
#                           c(glb_rsp_var, "NewsDesk", "SectionName", "SubsectionName")))

# print(table(glb_allobs_df$NewsDesk, glb_allobs_df$SectionName))
# print(table(glb_allobs_df$SectionName, glb_allobs_df$SubsectionName))
# print(table(glb_allobs_df$NewsDesk, glb_allobs_df$SectionName, glb_allobs_df$SubsectionName))

# glb_allobs_df$myCategory.fctr <- as.factor(glb_allobs_df$myCategory)
# glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, 
#                                       c("myCategory", "NewsDesk", "SectionName", "SubsectionName"))

# Copy Headline into Snipper & Abstract if they are empty
# print(glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, c("Headline", "Snippet")])
# print(glb_allobs_df[glb_allobs_df$Headline == glb_allobs_df$Snippet, 
#                     c("UniqueID", "Headline", "Snippet")])
# glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, "Snippet"] <- 
#     glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, "Headline"]
# 
# print(glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, c("Headline", "Abstract")])
# print(glb_allobs_df[glb_allobs_df$Headline == glb_allobs_df$Abstract, 
#                     c("UniqueID", "Headline", "Abstract")])
# glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, "Abstract"] <- 
#     glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, "Headline"]

# WordCount_0_df <- subset(glb_allobs_df, WordCount == 0)
# table(WordCount_0_df$Popular, WordCount_0_df$WordCount, useNA="ifany")
# myprint_df(WordCount_0_df[, 
#                 c("UniqueID", "Popular", "WordCount", "Headline")])

Step 2.1: scrub data

glb_chunks_df <- myadd_chunk(glb_chunks_df, "transform.data", major.inc=FALSE)
##            label step_major step_minor    bgn    end elapsed
## 3     scrub.data          2          1 20.290 21.385   1.096
## 4 transform.data          2          2 21.386     NA      NA
### Mapping dictionary
#sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
if (!is.null(glb_map_vars)) {
    for (feat in glb_map_vars) {
        map_df <- myimport_data(url=glb_map_urls[[feat]], 
                                            comment="map_df", 
                                           print_diagn=TRUE)
        glb_allobs_df <- mymap_codes(glb_allobs_df, feat, names(map_df)[2], 
                                     map_df, map_join_col_name=names(map_df)[1], 
                                     map_tgt_col_name=names(map_df)[2])
    }
    glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_map_vars)
}

### Forced Assignments
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
for (feat in glb_assign_vars) {
    new_feat <- paste0(feat, ".my")
    print(sprintf("Forced Assignments for: %s -> %s...", feat, new_feat))
    glb_allobs_df[, new_feat] <- glb_allobs_df[, feat]
    
    pairs <- glb_assign_pairs_lst[[feat]]
    for (pair_ix in 1:length(pairs$from)) {
        if (is.na(pairs$from[pair_ix]))
            nobs <- nrow(filter(glb_allobs_df, 
                                is.na(eval(parse(text=feat),
                                            envir=glb_allobs_df)))) else
            nobs <- sum(glb_allobs_df[, feat] == pairs$from[pair_ix])
        #nobs <- nrow(filter(glb_allobs_df, is.na(Married.fctr)))    ; print(nobs)
        
        if ((is.na(pairs$from[pair_ix])) && (is.na(pairs$to[pair_ix])))
            stop("what are you trying to do ???")
        if (is.na(pairs$from[pair_ix]))
            glb_allobs_df[is.na(glb_allobs_df[, feat]), new_feat] <- 
                pairs$to[pair_ix] else
            glb_allobs_df[glb_allobs_df[, feat] == pairs$from[pair_ix], new_feat] <- 
                pairs$to[pair_ix]
                    
        print(sprintf("    %s -> %s for %s obs", 
                      pairs$from[pair_ix], pairs$to[pair_ix], format(nobs, big.mark=",")))
    }

    glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_assign_vars)
}

### Derivations using mapping functions
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
for (new_feat in glb_derive_vars) {
    print(sprintf("Creating new feature: %s...", new_feat))
    args_lst <- NULL 
    for (arg in glb_derive_lst[[new_feat]]$args) 
        args_lst[[arg]] <- glb_allobs_df[, arg]
    glb_allobs_df[, new_feat] <- do.call(glb_derive_lst[[new_feat]]$mapfn, args_lst)
}
## [1] "Creating new feature: state.fctr..."
## [1] "Creating new feature: crime.fctr..."

Step 2.2: transform data

#```{r extract_features, cache=FALSE, eval=!is.null(glb_txt_vars)}
glb_chunks_df <- myadd_chunk(glb_chunks_df, "extract.features", major.inc=TRUE)
##              label step_major step_minor    bgn    end elapsed
## 4   transform.data          2          2 21.386 21.453   0.067
## 5 extract.features          3          0 21.454     NA      NA
extract.features_chunk_df <- myadd_chunk(NULL, "extract.features_bgn")
##                  label step_major step_minor   bgn end elapsed
## 1 extract.features_bgn          1          0 21.46  NA      NA
# Options:
#   Select Tf, log(1 + Tf), Tf-IDF or BM25Tf-IDf

# Create new features that help prediction
# <col_name>.lag.2 <- lag(zoo(glb_trnobs_df$<col_name>), -2, na.pad=TRUE)
# glb_trnobs_df[, "<col_name>.lag.2"] <- coredata(<col_name>.lag.2)
# <col_name>.lag.2 <- lag(zoo(glb_newobs_df$<col_name>), -2, na.pad=TRUE)
# glb_newobs_df[, "<col_name>.lag.2"] <- coredata(<col_name>.lag.2)
# 
# glb_newobs_df[1, "<col_name>.lag.2"] <- glb_trnobs_df[nrow(glb_trnobs_df) - 1, 
#                                                    "<col_name>"]
# glb_newobs_df[2, "<col_name>.lag.2"] <- glb_trnobs_df[nrow(glb_trnobs_df), 
#                                                    "<col_name>"]
                                                   
# glb_allobs_df <- mutate(glb_allobs_df,
#     A.P.http=ifelse(grepl("http",Added,fixed=TRUE), 1, 0)
#                     )
# 
# glb_trnobs_df <- mutate(glb_trnobs_df,
#                     )
# 
# glb_newobs_df <- mutate(glb_newobs_df,
#                     )

#   Convert dates to numbers 
#       typically, dates come in as chars; 
#           so this must be done before converting chars to factors

#stop(here"); sav_allobs_df <- glb_allobs_df #; glb_allobs_df <- sav_allobs_df
if (!is.null(glb_date_vars)) {
    glb_allobs_df <- cbind(glb_allobs_df, 
        myextract_dates_df(df=glb_allobs_df, vars=glb_date_vars, 
                           id_vars=glb_id_var, rsp_var=glb_rsp_var))
    for (sfx in c("", ".POSIX"))
        glb_exclude_vars_as_features <- 
            union(glb_exclude_vars_as_features, 
                    paste(glb_date_vars, sfx, sep=""))

    for (feat in glb_date_vars) {
        glb_allobs_df <- orderBy(reformulate(paste0(feat, ".POSIX")), glb_allobs_df)
#         print(myplot_scatter(glb_allobs_df, xcol_name=paste0(feat, ".POSIX"),
#                              ycol_name=glb_rsp_var, colorcol_name=glb_rsp_var))
        print(myplot_scatter(glb_allobs_df[glb_allobs_df[, paste0(feat, ".POSIX")] >=
                                               strptime("2012-12-01", "%Y-%m-%d"), ], 
                             xcol_name=paste0(feat, ".POSIX"),
                             ycol_name=glb_rsp_var, colorcol_name=paste0(feat, ".wkend")))

        # Create features that measure the gap between previous timestamp in the data
        require(zoo)
        z <- zoo(as.numeric(as.POSIXlt(glb_allobs_df[, paste0(feat, ".POSIX")])))
        glb_allobs_df[, paste0(feat, ".zoo")] <- z
        print(head(glb_allobs_df[, c(glb_id_var, feat, paste0(feat, ".zoo"))]))
        print(myplot_scatter(glb_allobs_df[glb_allobs_df[,  paste0(feat, ".POSIX")] >
                                            strptime("2012-10-01", "%Y-%m-%d"), ], 
                            xcol_name=paste0(feat, ".zoo"), ycol_name=glb_rsp_var,
                            colorcol_name=glb_rsp_var))
        b <- zoo(, seq(nrow(glb_allobs_df)))
        
        last1 <- as.numeric(merge(z-lag(z, -1), b, all=TRUE)); last1[is.na(last1)] <- 0
        glb_allobs_df[, paste0(feat, ".last1.log")] <- log(1 + last1)
        print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[, 
                                                    paste0(feat, ".last1.log")] > 0, ], 
                               ycol_names=paste0(feat, ".last1.log"), 
                               xcol_name=glb_rsp_var))
        
        last2 <- as.numeric(merge(z-lag(z, -2), b, all=TRUE)); last2[is.na(last2)] <- 0
        glb_allobs_df[, paste0(feat, ".last2.log")] <- log(1 + last2)
        print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[, 
                                                    paste0(feat, ".last2.log")] > 0, ], 
                               ycol_names=paste0(feat, ".last2.log"), 
                               xcol_name=glb_rsp_var))
        
        last10 <- as.numeric(merge(z-lag(z, -10), b, all=TRUE)); last10[is.na(last10)] <- 0
        glb_allobs_df[, paste0(feat, ".last10.log")] <- log(1 + last10)
        print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[, 
                                                    paste0(feat, ".last10.log")] > 0, ], 
                               ycol_names=paste0(feat, ".last10.log"), 
                               xcol_name=glb_rsp_var))
        
        last100 <- as.numeric(merge(z-lag(z, -100), b, all=TRUE)); last100[is.na(last100)] <- 0
        glb_allobs_df[, paste0(feat, ".last100.log")] <- log(1 + last100)
        print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[, 
                                                    paste0(feat, ".last100.log")] > 0, ], 
                               ycol_names=paste0(feat, ".last100.log"), 
                               xcol_name=glb_rsp_var))
        
        glb_allobs_df <- orderBy(reformulate(glb_id_var), glb_allobs_df)
        glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, 
                                                c(paste0(feat, ".zoo")))
        # all2$last3 = as.numeric(merge(z-lag(z, -3), b, all = TRUE))
        # all2$last5 = as.numeric(merge(z-lag(z, -5), b, all = TRUE))
        # all2$last10 = as.numeric(merge(z-lag(z, -10), b, all = TRUE))
        # all2$last20 = as.numeric(merge(z-lag(z, -20), b, all = TRUE))
        # all2$last50 = as.numeric(merge(z-lag(z, -50), b, all = TRUE))
        # 
        # 
        # # order table
        # all2 = all2[order(all2$id),]
        # 
        # ## fill in NAs
        # # count averages
        # na.avg = all2 %>% group_by(weekend, hour) %>% dplyr::summarise(
        #     last1=mean(last1, na.rm=TRUE),
        #     last3=mean(last3, na.rm=TRUE),
        #     last5=mean(last5, na.rm=TRUE),
        #     last10=mean(last10, na.rm=TRUE),
        #     last20=mean(last20, na.rm=TRUE),
        #     last50=mean(last50, na.rm=TRUE)
        # )
        # 
        # # fill in averages
        # na.merge = merge(all2, na.avg, by=c("weekend","hour"))
        # na.merge = na.merge[order(na.merge$id),]
        # for(i in c("last1", "last3", "last5", "last10", "last20", "last50")) {
        #     y = paste0(i, ".y")
        #     idx = is.na(all2[[i]])
        #     all2[idx,][[i]] <- na.merge[idx,][[y]]
        # }
        # rm(na.avg, na.merge, b, i, idx, n, pd, sec, sh, y, z)
    }
}
rm(last1, last10, last100)
## Warning in rm(last1, last10, last100): object 'last1' not found
## Warning in rm(last1, last10, last100): object 'last10' not found
## Warning in rm(last1, last10, last100): object 'last100' not found
#   Create factors of string variables
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
            paste0("extract.features_", "factorize.str.vars"), major.inc=TRUE)
##                                 label step_major step_minor    bgn    end
## 1                extract.features_bgn          1          0 21.460 21.475
## 2 extract.features_factorize.str.vars          2          0 21.476     NA
##   elapsed
## 1   0.015
## 2      NA
#stop(here"); sav_allobs_df <- glb_allobs_df; #glb_allobs_df <- sav_allobs_df
print(str_vars <- myfind_chr_cols_df(glb_allobs_df))
##        .src   .rownames 
##      ".src" ".rownames"
if (length(str_vars <- setdiff(str_vars, 
                               c(glb_exclude_vars_as_features, glb_txt_vars))) > 0) {
    for (var in str_vars) {
        warning("Creating factors of string variable: ", var, 
                ": # of unique values: ", length(unique(glb_allobs_df[, var])))
        glb_allobs_df[, paste0(var, ".fctr")] <- 
            relevel(factor(glb_allobs_df[, var]),
                    names(which.max(table(glb_allobs_df[, var], useNA = "ifany"))))
    }
    glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, str_vars)
}

if (!is.null(glb_txt_vars)) {
    require(foreach)
    require(gsubfn)
    require(stringr)
    require(tm)
    
    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
            paste0("extract.features_", "process.text"), major.inc=TRUE)
    
    chk_pattern_freq <- function(rex_str, ignore.case=TRUE) {
        match_mtrx <- str_extract_all(txt_vctr, regex(rex_str, ignore_case=ignore.case), 
                                      simplify=TRUE)
        match_df <- as.data.frame(match_mtrx[match_mtrx != ""])
        names(match_df) <- "pattern"
        return(mycreate_sqlxtab_df(match_df, "pattern"))        
    }

#     match_lst <- gregexpr("\\bok(?!ay)", txt_vctr[746], ignore.case = FALSE, perl=TRUE); print(match_lst)
    dsp_pattern <- function(rex_str, ignore.case=TRUE, print.all=TRUE) {
        match_lst <- gregexpr(rex_str, txt_vctr, ignore.case = ignore.case, perl=TRUE)
        match_lst <- regmatches(txt_vctr, match_lst)
        match_df <- data.frame(matches=sapply(match_lst, 
                                              function (elems) paste(elems, collapse="#")))
        match_df <- subset(match_df, matches != "")
        if (print.all)
            print(match_df)
        return(match_df)
    }
    
    dsp_matches <- function(rex_str, ix) {
        print(match_pos <- gregexpr(rex_str, txt_vctr[ix], perl=TRUE))
        print(str_sub(txt_vctr[ix], (match_pos[[1]] / 100) *  99 +   0, 
                                    (match_pos[[1]] / 100) * 100 + 100))        
    }

    myapply_gsub <- function(...) {
        if ((length_lst <- length(names(gsub_map_lst))) == 0)
            return(txt_vctr)
        for (ptn_ix in 1:length_lst) {
            if ((ptn_ix %% 10) == 0)
                print(sprintf("running gsub for %02d (of %02d): #%s#...", ptn_ix, 
                                length(names(gsub_map_lst)), names(gsub_map_lst)[ptn_ix]))
            txt_vctr <- gsub(names(gsub_map_lst)[ptn_ix], gsub_map_lst[[ptn_ix]], 
                               txt_vctr, ...)
        }
        return(txt_vctr)
    }    

    myapply_txtmap <- function(txt_vctr, ...) {
        nrows <- nrow(glb_txt_map_df)
        for (ptn_ix in 1:nrows) {
            if ((ptn_ix %% 10) == 0)
                print(sprintf("running gsub for %02d (of %02d): #%s#...", ptn_ix, 
                                nrows, glb_txt_map_df[ptn_ix, "rex_str"]))
            txt_vctr <- gsub(glb_txt_map_df[ptn_ix, "rex_str"], 
                             glb_txt_map_df[ptn_ix, "rpl_str"], 
                               txt_vctr, ...)
        }
        return(txt_vctr)
    }    

    chk.equal <- function(bgn, end) {
        print(all.equal(sav_txt_lst[["Headline"]][bgn:end], 
                        glb_txt_lst[["Headline"]][bgn:end]))
    }    
    dsp.equal <- function(bgn, end) {
        print(sav_txt_lst[["Headline"]][bgn:end])
        print(glb_txt_lst[["Headline"]][bgn:end])
    }    
#sav_txt_lst <- glb_txt_lst; all.equal(sav_txt_lst, glb_txt_lst)
#all.equal(sav_txt_lst[["Headline"]][1:4200], glb_txt_lst[["Headline"]][1:4200])
#chk.equal( 1, 100)
#dsp.equal(86, 90)
    
    glb_txt_map_df <- read.csv("mytxt_map.csv", comment.char="#", strip.white=TRUE)
    glb_txt_lst <- list(); 
    print(sprintf("Building glb_txt_lst..."))
    glb_txt_lst <- foreach(txt_var=glb_txt_vars) %dopar% {   
#     for (txt_var in glb_txt_vars) {
        txt_vctr <- glb_allobs_df[, txt_var]
        
        # myapply_txtmap shd be created as a tm_map::content_transformer ?
        #print(glb_txt_map_df)
        #txt_var=glb_txt_vars[3]; txt_vctr <- glb_txt_lst[[txt_var]]
        #print(rex_str <- glb_txt_map_df[163, "rex_str"])
        #print(rex_str <- glb_txt_map_df[glb_txt_map_df$rex_str == "\\bWall St\\.", "rex_str"])
        #print(rex_str <- glb_txt_map_df[grepl("du Pont", glb_txt_map_df$rex_str), "rex_str"])        
        #print(rex_str <- glb_txt_map_df[glb_txt_map_df$rpl_str == "versus", "rex_str"])             
        #print(tmp_vctr <- grep(rex_str, txt_vctr, value=TRUE, ignore.case=FALSE))
        #ret_lst <- regexec(rex_str, txt_vctr, ignore.case=FALSE); ret_lst <- regmatches(txt_vctr, ret_lst); ret_vctr <- sapply(1:length(ret_lst), function(pos_ix) ifelse(length(ret_lst[[pos_ix]]) > 0, ret_lst[[pos_ix]], "")); print(ret_vctr <- ret_vctr[ret_vctr != ""])
        #gsub(rex_str, glb_txt_map_df[glb_txt_map_df$rex_str == rex_str, "rpl_str"], tmp_vctr, ignore.case=FALSE)
        #grep("Hong Hong", txt_vctr, value=TRUE)
    
        txt_vctr <- myapply_txtmap(txt_vctr, ignore.case=FALSE)    
    }
    names(glb_txt_lst) <- glb_txt_vars

    for (txt_var in glb_txt_vars) {
        print(sprintf("Remaining OK in %s:", txt_var))
        txt_vctr <- glb_txt_lst[[txt_var]]
        
        print(chk_pattern_freq(rex_str <- "(?<!(BO|HO|LO))OK(?!(E\\!|ED|IE|IN|S ))",
                               ignore.case=FALSE))
        match_df <- dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
        for (row in row.names(match_df))
            dsp_matches(rex_str, ix=as.numeric(row))

        print(chk_pattern_freq(rex_str <- "Ok(?!(a\\.|ay|in|ra|um))", ignore.case=FALSE))
        match_df <- dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
        for (row in row.names(match_df))
            dsp_matches(rex_str, ix=as.numeric(row))

        print(chk_pattern_freq(rex_str <- "(?<!( b| B| c| C| g| G| j| M| p| P| w| W| r| Z|\\(b|ar|bo|Bo|co|Co|Ew|gk|go|ho|ig|jo|kb|ke|Ke|ki|lo|Lo|mo|mt|no|No|po|ra|ro|sm|Sm|Sp|to|To))ok(?!(ay|bo|e |e\\)|e,|e\\.|eb|ed|el|en|er|es|ey|i |ie|in|it|ka|ke|ki|ly|on|oy|ra|st|u |uc|uy|yl|yo))",
                               ignore.case=FALSE))
        match_df <- dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
        for (row in row.names(match_df))
            dsp_matches(rex_str, ix=as.numeric(row))
    }    
    # txt_vctr <- glb_txt_lst[[glb_txt_vars[1]]]
    # print(chk_pattern_freq(rex_str <- "(?<!( b| c| C| p|\\(b|bo|co|lo|Lo|Sp|to|To))ok(?!(ay|e |e\\)|e,|e\\.|ed|el|en|es|ey|ie|in|on|ra))", ignore.case=FALSE))
    # print(chk_pattern_freq(rex_str <- "ok(?!(ay|el|on|ra))", ignore.case=FALSE))
    # dsp_pattern(rex_str, ignore.case=FALSE, print.all=FALSE)
    # dsp_matches(rex_str, ix=8)
    # substr(txt_vctr[86], 5613, 5620)
    # substr(glb_allobs_df[301, "review"], 550, 650)

#stop(here"); sav_txt_lst <- glb_txt_lst    
    for (txt_var in glb_txt_vars) {
        print(sprintf("Remaining Acronyms in %s:", txt_var))
        txt_vctr <- glb_txt_lst[[txt_var]]
        
        print(chk_pattern_freq(rex_str <- "([[:upper:]]\\.( *)){2,}", ignore.case=FALSE))
        
        # Check for names
        print(subset(chk_pattern_freq(rex_str <- "(([[:upper:]]+)\\.( *)){1}",
                                      ignore.case=FALSE),
                     .n > 1))
        # dsp_pattern(rex_str="(OK\\.( *)){1}", ignore.case=FALSE)
        # dsp_matches(rex_str="(OK\\.( *)){1}", ix=557)
        #dsp_matches(rex_str="\\bR\\.I\\.P(\\.*)(\\B)", ix=461)
        #dsp_matches(rex_str="\\bR\\.I\\.P(\\.*)", ix=461)        
        #print(str_sub(txt_vctr[676], 10100, 10200))
        #print(str_sub(txt_vctr[74], 1, -1))        
    }

    for (txt_var in glb_txt_vars) {
        re_str <- "\\b(Fort|Ft\\.|Hong|Las|Los|New|Puerto|Saint|San|St\\.)( |-)(\\w)+"
        print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
        txt_vctr <- glb_txt_lst[[txt_var]]        
        print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE), 
                                             grepl("( |-)[[:upper:]]", pattern))))
        print("    consider cleaning if relevant to problem domain; geography name; .n > 1")
        #grep("New G", txt_vctr, value=TRUE, ignore.case=FALSE)
        #grep("St\\. Wins", txt_vctr, value=TRUE, ignore.case=FALSE)
    }        
        
#stop(here"); sav_txt_lst <- glb_txt_lst    
    for (txt_var in glb_txt_vars) {
        re_str <- "\\b(N|S|E|W|C)( |\\.)(\\w)+"
        print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))        
        txt_vctr <- glb_txt_lst[[txt_var]]                
        print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE), 
                                             grepl(".", pattern))))
        #grep("N Weaver", txt_vctr, value=TRUE, ignore.case=FALSE)        
    }    

    for (txt_var in glb_txt_vars) {
        re_str <- "\\b(North|South|East|West|Central)( |\\.)(\\w)+"
        print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))        
        txt_vctr <- glb_txt_lst[[txt_var]]                        
        print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE), 
                                             grepl(".", pattern))))
        #grep("Central (African|Bankers|Cast|Italy|Role|Spring)", txt_vctr, value=TRUE, ignore.case=FALSE)
        #grep("East (Africa|Berlin|London|Poland|Rivals|Spring)", txt_vctr, value=TRUE, ignore.case=FALSE)
        #grep("North (American|Korean|West)", txt_vctr, value=TRUE, ignore.case=FALSE)        
        #grep("South (Pacific|Street)", txt_vctr, value=TRUE, ignore.case=FALSE)
        #grep("St\\. Martins", txt_vctr, value=TRUE, ignore.case=FALSE)
    }    

    find_cmpnd_wrds <- function(txt_vctr) {
        txt_corpus <- Corpus(VectorSource(txt_vctr))
        txt_corpus <- tm_map(txt_corpus, tolower)
        txt_corpus <- tm_map(txt_corpus, PlainTextDocument)
        txt_corpus <- tm_map(txt_corpus, removePunctuation, 
                             preserve_intra_word_dashes=TRUE)
        full_Tf_DTM <- DocumentTermMatrix(txt_corpus, 
                                          control=list(weighting=weightTf))
        print("   Full TermMatrix:"); print(full_Tf_DTM)
        full_Tf_mtrx <- as.matrix(full_Tf_DTM)
        rownames(full_Tf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
        full_Tf_vctr <- colSums(full_Tf_mtrx)
        names(full_Tf_vctr) <- dimnames(full_Tf_DTM)[[2]]
        #grep("year", names(full_Tf_vctr), value=TRUE)
        #which.max(full_Tf_mtrx[, "yearlong"])
        full_Tf_df <- as.data.frame(full_Tf_vctr)
        names(full_Tf_df) <- "Tf.full"
        full_Tf_df$term <- rownames(full_Tf_df)
        #full_Tf_df$freq.full <- colSums(full_Tf_mtrx != 0)
        full_Tf_df <- orderBy(~ -Tf.full, full_Tf_df)
        cmpnd_Tf_df <- full_Tf_df[grep("-", full_Tf_df$term, value=TRUE) ,]
        
        filter_df <- read.csv("mytxt_compound.csv", comment.char="#", strip.white=TRUE)
        cmpnd_Tf_df$filter <- FALSE
        for (row_ix in 1:nrow(filter_df))
            cmpnd_Tf_df[!cmpnd_Tf_df$filter, "filter"] <- 
            grepl(filter_df[row_ix, "rex_str"], 
                  cmpnd_Tf_df[!cmpnd_Tf_df$filter, "term"], ignore.case=TRUE)
        cmpnd_Tf_df <- subset(cmpnd_Tf_df, !filter)
        # Bug in tm_map(txt_corpus, removePunctuation, preserve_intra_word_dashes=TRUE) ???
        #   "net-a-porter" gets converted to "net-aporter"
        #grep("net-a-porter", txt_vctr, ignore.case=TRUE, value=TRUE)
        #grep("maser-laser", txt_vctr, ignore.case=TRUE, value=TRUE)
        #txt_corpus[[which(grepl("net-a-porter", txt_vctr, ignore.case=TRUE))]]
        #grep("\\b(across|longer)-(\\w)", cmpnd_Tf_df$term, ignore.case=TRUE, value=TRUE)
        #grep("(\\w)-(affected|term)\\b", cmpnd_Tf_df$term, ignore.case=TRUE, value=TRUE)
        
        print(sprintf("nrow(cmpnd_Tf_df): %d", nrow(cmpnd_Tf_df)))
        myprint_df(cmpnd_Tf_df)
    }

    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
            paste0("extract.features_", "process.text_reporting_compound_terms"), major.inc=FALSE)
    
    for (txt_var in glb_txt_vars) {
        print(sprintf("Remaining compound terms in %s: ", txt_var))        
        txt_vctr <- glb_txt_lst[[txt_var]]                        
#         find_cmpnd_wrds(txt_vctr)
        #grep("thirty-five", txt_vctr, ignore.case=TRUE, value=TRUE)
        #rex_str <- glb_txt_map_df[grepl("hirty", glb_txt_map_df$rex_str), "rex_str"]
    }

    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
            paste0("extract.features_", "build.corpus"), major.inc=TRUE)
    
    glb_corpus_lst <- list()
    print(sprintf("Building glb_corpus_lst..."))
    glb_corpus_lst <- foreach(txt_var=glb_txt_vars) %dopar% {   
#     for (txt_var in glb_txt_vars) {
        txt_corpus <- Corpus(VectorSource(glb_txt_lst[[txt_var]]))
        txt_corpus <- tm_map(txt_corpus, tolower) #nuppr
        txt_corpus <- tm_map(txt_corpus, PlainTextDocument)
        txt_corpus <- tm_map(txt_corpus, removePunctuation) #npnct<chr_ix>
#         txt-corpus <- tm_map(txt_corpus, content_transformer(function(x, pattern) gsub(pattern, "", x))   

        # Not to be run in production
        inspect_terms <- function() {
            full_Tf_DTM <- DocumentTermMatrix(txt_corpus, 
                                              control=list(weighting=weightTf))
            print("   Full TermMatrix:"); print(full_Tf_DTM)
            full_Tf_mtrx <- as.matrix(full_Tf_DTM)
            rownames(full_Tf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
            full_Tf_vctr <- colSums(full_Tf_mtrx)
            names(full_Tf_vctr) <- dimnames(full_Tf_DTM)[[2]]
            #grep("year", names(full_Tf_vctr), value=TRUE)
            #which.max(full_Tf_mtrx[, "yearlong"])
            full_Tf_df <- as.data.frame(full_Tf_vctr)
            names(full_Tf_df) <- "Tf.full"
            full_Tf_df$term <- rownames(full_Tf_df)
            #full_Tf_df$freq.full <- colSums(full_Tf_mtrx != 0)
            full_Tf_df <- orderBy(~ -Tf.full +term, full_Tf_df)
            print(myplot_histogram(full_Tf_df, "Tf.full"))
            myprint_df(full_Tf_df)
            #txt_corpus[[which(grepl("zun", txt_vctr, ignore.case=TRUE))]]
            digit_terms_df <- subset(full_Tf_df, grepl("[[:digit:]]", term))
            myprint_df(digit_terms_df)
            return(full_Tf_df)
        }    
        #print("RemovePunct:"); remove_punct_Tf_df <- inspect_terms()

        txt_corpus <- tm_map(txt_corpus, removeWords, 
                             c(glb_append_stop_words[[txt_var]], 
                               stopwords("english"))) #nstopwrds
        #print("StoppedWords:"); stopped_words_Tf_df <- inspect_terms()
        txt_corpus <- tm_map(txt_corpus, stemDocument) #Features for lost information: Difference/ratio in density of full_TfIdf_DTM ???
        #txt_corpus <- tm_map(txt_corpus, content_transformer(stemDocument))        
        #print("StemmedWords:"); stemmed_words_Tf_df <- inspect_terms()
        #stemmed_stopped_Tf_df <- merge(stemmed_words_Tf_df, stopped_words_Tf_df, by="term", all=TRUE, suffixes=c(".stem", ".stop"))
        #myprint_df(stemmed_stopped_Tf_df)
        #print(subset(stemmed_stopped_Tf_df, grepl("compan", term)))
        #glb_corpus_lst[[txt_var]] <- txt_corpus
    }
    names(glb_corpus_lst) <- glb_txt_vars
        
    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
            paste0("extract.features_", "extract.DTM"), major.inc=TRUE)

    glb_full_DTM_lst <- list(); glb_sprs_DTM_lst <- list();
    for (txt_var in glb_txt_vars) {
        print(sprintf("Extracting TfIDf terms for %s...", txt_var))        
        txt_corpus <- glb_corpus_lst[[txt_var]]
        
#         full_Tf_DTM <- DocumentTermMatrix(txt_corpus, 
#                                           control=list(weighting=weightTf))
        full_TfIdf_DTM <- DocumentTermMatrix(txt_corpus, 
                                          control=list(weighting=weightTfIdf))
        sprs_TfIdf_DTM <- removeSparseTerms(full_TfIdf_DTM, 
                                            glb_sprs_thresholds[txt_var])
        
#         glb_full_DTM_lst[[txt_var]] <- full_Tf_DTM
#         glb_sprs_DTM_lst[[txt_var]] <- sprs_Tf_DTM
        glb_full_DTM_lst[[txt_var]] <- full_TfIdf_DTM
        glb_sprs_DTM_lst[[txt_var]] <- sprs_TfIdf_DTM
    }

    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
            paste0("extract.features_", "report.DTM"), major.inc=TRUE)
    
    for (txt_var in glb_txt_vars) {
        print(sprintf("Reporting TfIDf terms for %s...", txt_var))        
        full_TfIdf_DTM <- glb_full_DTM_lst[[txt_var]]
        sprs_TfIdf_DTM <- glb_sprs_DTM_lst[[txt_var]]        

        print("   Full TermMatrix:"); print(full_TfIdf_DTM)
        full_TfIdf_mtrx <- as.matrix(full_TfIdf_DTM)
        rownames(full_TfIdf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
        full_TfIdf_vctr <- colSums(full_TfIdf_mtrx)
        names(full_TfIdf_vctr) <- dimnames(full_TfIdf_DTM)[[2]]
        #grep("scene", names(full_TfIdf_vctr), value=TRUE)
        #which.max(full_TfIdf_mtrx[, "yearlong"])
        full_TfIdf_df <- as.data.frame(full_TfIdf_vctr)
        names(full_TfIdf_df) <- "TfIdf.full"
        full_TfIdf_df$term <- rownames(full_TfIdf_df)
        full_TfIdf_df$freq.full <- colSums(full_TfIdf_mtrx != 0)
        full_TfIdf_df <- orderBy(~ -TfIdf.full, full_TfIdf_df)

        print("   Sparse TermMatrix:"); print(sprs_TfIdf_DTM)
        sprs_TfIdf_vctr <- colSums(as.matrix(sprs_TfIdf_DTM))
        names(sprs_TfIdf_vctr) <- dimnames(sprs_TfIdf_DTM)[[2]]
        sprs_TfIdf_df <- as.data.frame(sprs_TfIdf_vctr)
        names(sprs_TfIdf_df) <- "TfIdf.sprs"
        sprs_TfIdf_df$term <- rownames(sprs_TfIdf_df)
        sprs_TfIdf_df$freq.sprs <- colSums(as.matrix(sprs_TfIdf_DTM) != 0)        
        sprs_TfIdf_df <- orderBy(~ -TfIdf.sprs, sprs_TfIdf_df)
        
        terms_TfIdf_df <- merge(full_TfIdf_df, sprs_TfIdf_df, all.x=TRUE)
        terms_TfIdf_df$in.sprs <- !is.na(terms_TfIdf_df$freq.sprs)
        plt_TfIdf_df <- subset(terms_TfIdf_df, 
                               TfIdf.full >= min(terms_TfIdf_df$TfIdf.sprs, na.rm=TRUE))
        plt_TfIdf_df$label <- ""
        plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "label"] <- 
            plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "term"]
        glb_important_terms[[txt_var]] <- union(glb_important_terms[[txt_var]],
            plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "term"])
        print(myplot_scatter(plt_TfIdf_df, "freq.full", "TfIdf.full", 
                             colorcol_name="in.sprs") + 
                  geom_text(aes(label=label), color="Black", size=3.5))
        
        melt_TfIdf_df <- orderBy(~ -value, melt(terms_TfIdf_df, id.var="term"))
        print(ggplot(melt_TfIdf_df, aes(value, color=variable)) + stat_ecdf() + 
                  geom_hline(yintercept=glb_sprs_thresholds[txt_var], 
                             linetype = "dotted"))
        
        melt_TfIdf_df <- orderBy(~ -value, 
                        melt(subset(terms_TfIdf_df, !is.na(TfIdf.sprs)), id.var="term"))
        print(myplot_hbar(melt_TfIdf_df, "term", "value", 
                          colorcol_name="variable"))
        
        melt_TfIdf_df <- orderBy(~ -value, 
                        melt(subset(terms_TfIdf_df, is.na(TfIdf.sprs)), id.var="term"))
        print(myplot_hbar(head(melt_TfIdf_df, 10), "term", "value", 
                          colorcol_name="variable"))
    }

#     sav_full_DTM_lst <- glb_full_DTM_lst
#     sav_sprs_DTM_lst <- glb_sprs_DTM_lst
#     print(identical(sav_glb_corpus_lst, glb_corpus_lst))
#     print(all.equal(length(sav_glb_corpus_lst), length(glb_corpus_lst)))
#     print(all.equal(names(sav_glb_corpus_lst), names(glb_corpus_lst)))
#     print(all.equal(sav_glb_corpus_lst[["Headline"]], glb_corpus_lst[["Headline"]]))

#     print(identical(sav_full_DTM_lst, glb_full_DTM_lst))
#     print(identical(sav_sprs_DTM_lst, glb_sprs_DTM_lst))
        
    rm(full_TfIdf_mtrx, full_TfIdf_df, melt_TfIdf_df, terms_TfIdf_df)

    # Create txt features
    if ((length(glb_txt_vars) > 1) &&
        (length(unique(pfxs <- sapply(glb_txt_vars, 
                    function(txt) toupper(substr(txt, 1, 1))))) < length(glb_txt_vars)))
            stop("Prefixes for corpus freq terms not unique: ", pfxs)
    
    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
                            paste0("extract.features_", "bind.DTM"), 
                                         major.inc=TRUE)
    for (txt_var in glb_txt_vars) {
        print(sprintf("Binding DTM for %s...", txt_var))
        txt_var_pfx <- toupper(substr(txt_var, 1, 1))
        txt_X_df <- as.data.frame(as.matrix(glb_sprs_DTM_lst[[txt_var]]))
        colnames(txt_X_df) <- paste(txt_var_pfx, ".T.",
                                    make.names(colnames(txt_X_df)), sep="")
        rownames(txt_X_df) <- rownames(glb_allobs_df) # warning otherwise
#         plt_X_df <- cbind(txt_X_df, glb_allobs_df[, c(glb_id_var, glb_rsp_var)])
#         print(myplot_box(df=plt_X_df, ycol_names="H.T.today", xcol_name=glb_rsp_var))

#         log_X_df <- log(1 + txt_X_df)
#         colnames(log_X_df) <- paste(colnames(txt_X_df), ".log", sep="")
#         plt_X_df <- cbind(log_X_df, glb_allobs_df[, c(glb_id_var, glb_rsp_var)])
#         print(myplot_box(df=plt_X_df, ycol_names="H.T.today.log", xcol_name=glb_rsp_var))
        glb_allobs_df <- cbind(glb_allobs_df, txt_X_df) # TfIdf is normalized
        #glb_allobs_df <- cbind(glb_allobs_df, log_X_df) # if using non-normalized metrics 
    }
    #identical(chk_entity_df, glb_allobs_df)
    #chk_entity_df <- glb_allobs_df

    extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, 
                            paste0("extract.features_", "bind.DXM"), 
                                         major.inc=TRUE)

#sav_allobs_df <- glb_allobs_df
    glb_punct_vctr <- c("!", "\"", "#", "\\$", "%", "&", "'", 
                        "\\(|\\)",# "\\(", "\\)", 
                        "\\*", "\\+", ",", "-", "\\.", "/", ":", ";", 
                        "<|>", # "<", 
                        "=", 
                        # ">", 
                        "\\?", "@", "\\[", "\\\\", "\\]", "^", "_", "`", 
                        "\\{", "\\|", "\\}", "~")
    txt_X_df <- glb_allobs_df[, c(glb_id_var, ".rnorm"), FALSE]
    txt_X_df <- foreach(txt_var=glb_txt_vars, .combine=cbind) %dopar% {   
    #for (txt_var in glb_txt_vars) {
        print(sprintf("Binding DXM for %s...", txt_var))
        txt_var_pfx <- toupper(substr(txt_var, 1, 1))        
        #txt_X_df <- glb_allobs_df[, c(glb_id_var, ".rnorm"), FALSE]
        
        txt_full_DTM_mtrx <- as.matrix(glb_full_DTM_lst[[txt_var]])
        rownames(txt_full_DTM_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
        #print(txt_full_DTM_mtrx[txt_full_DTM_mtrx[, "ebola"] != 0, "ebola"])
        
        # Create <txt_var>.T.<term> for glb_important_terms
        for (term in glb_important_terms[[txt_var]])
            txt_X_df[, paste0(txt_var_pfx, ".T.", make.names(term))] <- 
                txt_full_DTM_mtrx[, term]
                
        # Create <txt_var>.nwrds.log & .nwrds.unq.log
        txt_X_df[, paste0(txt_var_pfx, ".nwrds.log")] <- 
            log(1 + mycount_pattern_occ("\\w+", glb_txt_lst[[txt_var]]))
        txt_X_df[, paste0(txt_var_pfx, ".nwrds.unq.log")] <- 
            log(1 + rowSums(txt_full_DTM_mtrx != 0))
        txt_X_df[, paste0(txt_var_pfx, ".sum.TfIdf")] <- 
            rowSums(txt_full_DTM_mtrx) 
        txt_X_df[, paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")] <- 
            txt_X_df[, paste0(txt_var_pfx, ".sum.TfIdf")] / 
            (exp(txt_X_df[, paste0(txt_var_pfx, ".nwrds.log")]) - 1)
        txt_X_df[is.nan(txt_X_df[, paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")]),
                 paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")] <- 0

        # Create <txt_var>.nchrs.log
        txt_X_df[, paste0(txt_var_pfx, ".nchrs.log")] <- 
            log(1 + mycount_pattern_occ(".", glb_allobs_df[, txt_var]))
        txt_X_df[, paste0(txt_var_pfx, ".nuppr.log")] <- 
            log(1 + mycount_pattern_occ("[[:upper:]]", glb_allobs_df[, txt_var]))
        txt_X_df[, paste0(txt_var_pfx, ".ndgts.log")] <- 
            log(1 + mycount_pattern_occ("[[:digit:]]", glb_allobs_df[, txt_var]))

        # Create <txt_var>.npnct?.log
        # would this be faster if it's iterated over each row instead of 
        #   each created column ???
        for (punct_ix in 1:length(glb_punct_vctr)) { 
#             smp0 <- " "
#             smp1 <- "! \" # $ % & ' ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ ` { | } ~"
#             smp2 <- paste(smp1, smp1, sep=" ")
#             print(sprintf("Testing %s pattern:", glb_punct_vctr[punct_ix])) 
#             results <- mycount_pattern_occ(glb_punct_vctr[punct_ix], c(smp0, smp1, smp2))
#             names(results) <- NULL; print(results)
            txt_X_df[, 
                paste0(txt_var_pfx, ".npnct", sprintf("%02d", punct_ix), ".log")] <-
                log(1 + mycount_pattern_occ(glb_punct_vctr[punct_ix], 
                                            glb_allobs_df[, txt_var]))
        }
#         print(head(glb_allobs_df[glb_allobs_df[, "A.npnct23.log"] > 0, 
#                                     c("UniqueID", "Popular", "Abstract", "A.npnct23.log")]))    
        
        # Create <txt_var>.nstopwrds.log & <txt_var>ratio.nstopwrds.nwrds
        stop_words_rex_str <- paste0("\\b(", paste0(c(glb_append_stop_words[[txt_var]], 
                                       stopwords("english")), collapse="|"),
                                     ")\\b")
        txt_X_df[, paste0(txt_var_pfx, ".nstopwrds", ".log")] <-
            log(1 + mycount_pattern_occ(stop_words_rex_str, glb_txt_lst[[txt_var]]))
        txt_X_df[, paste0(txt_var_pfx, ".ratio.nstopwrds.nwrds")] <-
            exp(txt_X_df[, paste0(txt_var_pfx, ".nstopwrds", ".log")] - 
                txt_X_df[, paste0(txt_var_pfx, ".nwrds", ".log")])

        # Create <txt_var>.P.http
        txt_X_df[, paste(txt_var_pfx, ".P.http", sep="")] <- 
            as.integer(0 + mycount_pattern_occ("http", glb_allobs_df[, txt_var]))    
    
        txt_X_df <- subset(txt_X_df, select=-.rnorm)
        txt_X_df <- txt_X_df[, -grep(glb_id_var, names(txt_X_df), fixed=TRUE), FALSE]
        #glb_allobs_df <- cbind(glb_allobs_df, txt_X_df)
    }
    glb_allobs_df <- cbind(glb_allobs_df, txt_X_df)
    #myplot_box(glb_allobs_df, "A.sum.TfIdf", glb_rsp_var)

    # Generate summaries
#     print(summary(glb_allobs_df))
#     print(sapply(names(glb_allobs_df), function(col) sum(is.na(glb_allobs_df[, col]))))
#     print(summary(glb_trnobs_df))
#     print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
#     print(summary(glb_newobs_df))
#     print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))

    glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, 
                                          glb_txt_vars)
    rm(log_X_df, txt_X_df)
}

# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))

# print(myplot_scatter(glb_trnobs_df, "<col1_name>", "<col2_name>", smooth=TRUE))

rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr, 
   glb_full_DTM_lst, glb_sprs_DTM_lst, txt_corpus, txt_vctr)
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'corpus_lst' not found
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'full_TfIdf_DTM' not found
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'full_TfIdf_vctr' not found
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'glb_full_DTM_lst' not found
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'glb_sprs_DTM_lst' not found
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'txt_corpus' not found
## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'txt_vctr' not found
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, "extract.features_end", 
                                     major.inc=TRUE)
##                                 label step_major step_minor    bgn    end
## 2 extract.features_factorize.str.vars          2          0 21.476 21.493
## 3                extract.features_end          3          0 21.494     NA
##   elapsed
## 2   0.018
## 3      NA
myplt_chunk(extract.features_chunk_df)
##                                 label step_major step_minor    bgn    end
## 2 extract.features_factorize.str.vars          2          0 21.476 21.493
## 1                extract.features_bgn          1          0 21.460 21.475
##   elapsed duration
## 2   0.018    0.017
## 1   0.015    0.015
## [1] "Total Elapsed Time: 21.493 secs"

# if (glb_save_envir)
#     save(glb_feats_df, 
#          glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
#          file=paste0(glb_out_pfx, "extract_features_dsk.RData"))
# load(paste0(glb_out_pfx, "extract_features_dsk.RData"))

replay.petrisim(pn=glb_analytics_pn, 
    replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs, 
        "data.training.all","data.new")), flip_coord=TRUE)
## time trans    "bgn " "fit.data.training.all " "predict.data.new " "end " 
## 0.0000   multiple enabled transitions:  data.training.all data.new model.selected    firing:  data.training.all 
## 1.0000    1   2 1 0 0 
## 1.0000   multiple enabled transitions:  data.training.all data.new model.selected model.final data.training.all.prediction   firing:  data.new 
## 2.0000    2   1 1 1 0

glb_chunks_df <- myadd_chunk(glb_chunks_df, "cluster.data", major.inc=TRUE)
##              label step_major step_minor    bgn    end elapsed
## 5 extract.features          3          0 21.454 22.799   1.345
## 6     cluster.data          4          0 22.800     NA      NA

Step 4.0: cluster data

glb_chunks_df <- myadd_chunk(glb_chunks_df, "manage.missing.data", major.inc=FALSE)
##                 label step_major step_minor    bgn    end elapsed
## 6        cluster.data          4          0 22.800 23.091   0.291
## 7 manage.missing.data          4          1 23.092     NA      NA
# If mice crashes with error: Error in get(as.character(FUN), mode = "function", envir = envir) : object 'State' of mode 'function' was not found
#   consider excluding 'State' as a feature

# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
# glb_trnobs_df <- na.omit(glb_trnobs_df)
# glb_newobs_df <- na.omit(glb_newobs_df)
# df[is.na(df)] <- 0

mycheck_problem_data(glb_allobs_df)
## [1] "numeric data missing in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ 0s in glb_allobs_df: "
##              male       time.served multiple.offenses          violator 
##               130                 1               313               597 
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## .rownames 
##         0
# glb_allobs_df <- na.omit(glb_allobs_df)

# Not refactored into mydsutils.R since glb_*_df might be reassigned
glb_impute_missing_data <- function() {
    
    require(mice)
    set.seed(glb_mice_complete.seed)
    inp_impent_df <- glb_allobs_df[, setdiff(names(glb_allobs_df), 
                                union(glb_exclude_vars_as_features, glb_rsp_var))]
    print("Summary before imputation: ")
    print(summary(inp_impent_df))
    out_impent_df <- complete(mice(inp_impent_df))
    print(summary(out_impent_df))
    
    ret_vars <- sapply(names(out_impent_df), 
                       function(col) ifelse(!identical(out_impent_df[, col],
                                                       inp_impent_df[, col]), 
                                            col, ""))
    ret_vars <- ret_vars[ret_vars != ""]
    
    # complete(mice()) changes attributes of factors even though values don't change
    for (col in ret_vars) {
        if (inherits(out_impent_df[, col], "factor")) {
            if (identical(as.numeric(out_impent_df[, col]), 
                          as.numeric(inp_impent_df[, col])))
                ret_vars <- setdiff(ret_vars, col)
        }
    }
    return(out_impent_df[, ret_vars])
}

if (glb_impute_na_data && 
    (length(myfind_numerics_missing(glb_allobs_df)) > 0) &&
    (ncol(nonna_df <- glb_impute_missing_data()) > 0)) {
    for (col in names(nonna_df)) {
        glb_allobs_df[, paste0(col, ".nonNA")] <- nonna_df[, col]
        glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, col)        
    }
}    
    
mycheck_problem_data(glb_allobs_df, terminate = TRUE)
## [1] "numeric data missing in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ 0s in glb_allobs_df: "
##              male       time.served multiple.offenses          violator 
##               130                 1               313               597 
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## .rownames 
##         0

Step 4.1: manage missing data

if (glb_cluster) {
    require(proxy)
    #require(hash)
    require(dynamicTreeCut)

#     glb_hash <- hash(key=unique(glb_allobs_df$myCategory), 
#                      values=1:length(unique(glb_allobs_df$myCategory)))
#     glb_hash_lst <- hash(key=unique(glb_allobs_df$myCategory), 
#                      values=1:length(unique(glb_allobs_df$myCategory)))
#stophere; sav_allobs_df <- glb_allobs_df; 
    print("Clustering features: ")
    print(cluster_vars <- grep("[HSA]\\.[PT]\\.", names(glb_allobs_df), value=TRUE))
    #print(cluster_vars <- grep("[HSA]\\.", names(glb_allobs_df), value=TRUE))
    glb_allobs_df$.clusterid <- 1    
    #print(max(table(glb_allobs_df$myCategory.fctr) / 20))
    for (myCategory in c("##", "Business#Business Day#Dealbook", "OpEd#Opinion#", 
                         "Styles#U.S.#", "Business#Technology#", "Science#Health#",
                         "Culture#Arts#")) {
        ctgry_allobs_df <- glb_allobs_df[glb_allobs_df$myCategory == myCategory, ]
        
        dstns_dist <- dist(ctgry_allobs_df[, cluster_vars], method = "cosine")
        dstns_mtrx <- as.matrix(dstns_dist)
        print(sprintf("max distance(%0.4f) pair:", max(dstns_mtrx)))
        row_ix <- ceiling(which.max(dstns_mtrx) / ncol(dstns_mtrx))
        col_ix <- which.max(dstns_mtrx[row_ix, ])
        print(ctgry_allobs_df[c(row_ix, col_ix), 
            c("UniqueID", "Popular", "myCategory", "Headline", cluster_vars)])
    
        min_dstns_mtrx <- dstns_mtrx
        diag(min_dstns_mtrx) <- 1
        print(sprintf("min distance(%0.4f) pair:", min(min_dstns_mtrx)))
        row_ix <- ceiling(which.min(min_dstns_mtrx) / ncol(min_dstns_mtrx))
        col_ix <- which.min(min_dstns_mtrx[row_ix, ])
        print(ctgry_allobs_df[c(row_ix, col_ix), 
            c("UniqueID", "Popular", "myCategory", "Headline", cluster_vars)])                          
    
        clusters <- hclust(dstns_dist, method = "ward.D2")
        #plot(clusters, labels=NULL, hang=-1)
        myplclust(clusters, lab.col=unclass(ctgry_allobs_df[, glb_rsp_var]))
        
        #clusterGroups = cutree(clusters, k=7)
        clusterGroups <- cutreeDynamic(clusters, minClusterSize=20, method="tree", deepSplit=0)
        # Unassigned groups are labeled 0; the largest group has label 1
        table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")   
        #print(ctgry_allobs_df[which(clusterGroups == 1), c("UniqueID", "Popular", "Headline")])
        #print(ctgry_allobs_df[(clusterGroups == 1) & !is.na(ctgry_allobs_df$Popular) & (ctgry_allobs_df$Popular==1), c("UniqueID", "Popular", "Headline")])
        clusterGroups[clusterGroups == 0] <- 1
        table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")        
        #summary(factor(clusterGroups))
#         clusterGroups <- clusterGroups + 
#                 100 * # has to be > max(table(glb_allobs_df$myCategory.fctr) / minClusterSize=20)
#                             which(levels(glb_allobs_df$myCategory.fctr) == myCategory)
#         table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")        
    
        # add to glb_allobs_df - then split the data again
        glb_allobs_df[glb_allobs_df$myCategory==myCategory,]$.clusterid <- clusterGroups
        #print(unique(glb_allobs_df$.clusterid))
        #print(glb_feats_df[glb_feats_df$id == ".clusterid.fctr", ])
    }
    
    ctgry_xtab_df <- orderBy(reformulate(c("-", ".n")),
                              mycreate_sqlxtab_df(glb_allobs_df,
        c("myCategory", ".clusterid", glb_rsp_var)))
    ctgry_cast_df <- orderBy(~ -Y -NA, dcast(ctgry_xtab_df, 
                           myCategory + .clusterid ~ 
                               Popular.fctr, sum, value.var=".n"))
    print(ctgry_cast_df)
    #print(orderBy(~ myCategory -Y -NA, ctgry_cast_df))
    # write.table(ctgry_cast_df, paste0(glb_out_pfx, "ctgry_clst.csv"), 
    #             row.names=FALSE)
    
    print(ctgry_sum_tbl <- table(glb_allobs_df$myCategory, glb_allobs_df$.clusterid, 
                                 glb_allobs_df[, glb_rsp_var], 
                                 useNA="ifany"))
#     dsp_obs(.clusterid=1, myCategory="OpEd#Opinion#", 
#             cols=c("UniqueID", "Popular", "myCategory", ".clusterid", "Headline"),
#             all=TRUE)
    
    glb_allobs_df$.clusterid.fctr <- as.factor(glb_allobs_df$.clusterid)
    glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, 
                                      ".clusterid")
    glb_interaction_only_features["myCategory.fctr"] <- c(".clusterid.fctr")
    glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, 
                                      cluster_vars)
}

# Last call for data modifications 
#stop(here") # sav_allobs_df <- glb_allobs_df
# glb_allobs_df[(glb_allobs_df$PropR == 0.75) & (glb_allobs_df$State == "Hawaii"), "PropR.fctr"] <- "N"

# Re-partition
glb_trnobs_df <- subset(glb_allobs_df, .src == "Train")
glb_newobs_df <- subset(glb_allobs_df, .src == "Test")

glb_chunks_df <- myadd_chunk(glb_chunks_df, "select.features", major.inc=TRUE)
##                 label step_major step_minor    bgn    end elapsed
## 7 manage.missing.data          4          1 23.092 23.158   0.066
## 8     select.features          5          0 23.158     NA      NA

Step 5.0: select features

print(glb_feats_df <- myselect_features(entity_df=glb_trnobs_df, 
                       exclude_vars_as_features=glb_exclude_vars_as_features, 
                       rsp_var=glb_rsp_var))
##                                  id        cor.y exclude.as.feat
## violator                   violator  1.000000000               1
## state                         state -0.164428672               1
## state.fctr               state.fctr -0.164428672               0
## max.sentence           max.sentence -0.107847018               0
## time.served             time.served -0.087969745               0
## multiple.offenses multiple.offenses  0.078350351               0
## race                           race  0.042966934               0
## crime                         crime -0.032695700               1
## crime.fctr               crime.fctr -0.032695700               0
## .rnorm                       .rnorm -0.023119508               0
## male                           male -0.019175165               0
## age                             age -0.008384572               0
##                     cor.y.abs
## violator          1.000000000
## state             0.164428672
## state.fctr        0.164428672
## max.sentence      0.107847018
## time.served       0.087969745
## multiple.offenses 0.078350351
## race              0.042966934
## crime             0.032695700
## crime.fctr        0.032695700
## .rnorm            0.023119508
## male              0.019175165
## age               0.008384572
# sav_feats_df <- glb_feats_df; glb_feats_df <- sav_feats_df
print(glb_feats_df <- orderBy(~-cor.y, 
          myfind_cor_features(feats_df=glb_feats_df, obs_df=glb_trnobs_df, 
                              rsp_var=glb_rsp_var)))
##                   id        cor.y exclude.as.feat   cor.y.abs cor.high.X
## 12          violator  1.000000000               1 1.000000000         NA
## 7  multiple.offenses  0.078350351               0 0.078350351         NA
## 8               race  0.042966934               0 0.042966934         NA
## 2                age -0.008384572               0 0.008384572         NA
## 5               male -0.019175165               0 0.019175165         NA
## 1             .rnorm -0.023119508               0 0.023119508         NA
## 3              crime -0.032695700               1 0.032695700         NA
## 4         crime.fctr -0.032695700               0 0.032695700         NA
## 11       time.served -0.087969745               0 0.087969745         NA
## 6       max.sentence -0.107847018               0 0.107847018         NA
## 9              state -0.164428672               1 0.164428672         NA
## 10        state.fctr -0.164428672               0 0.164428672         NA
##    freqRatio percentUnique zeroVar   nzv myNearZV is.cor.y.abs.low
## 12  7.600000      0.422833   FALSE FALSE    FALSE            FALSE
## 7   1.121076      0.422833   FALSE FALSE    FALSE            FALSE
## 8   1.413265      0.422833   FALSE FALSE    FALSE            FALSE
## 2   1.200000     54.756871   FALSE FALSE    FALSE             TRUE
## 5   4.564706      0.422833   FALSE FALSE    FALSE             TRUE
## 1   1.000000    100.000000   FALSE FALSE    FALSE            FALSE
## 3   2.235294      0.845666   FALSE FALSE    FALSE            FALSE
## 4   2.235294      0.845666   FALSE FALSE    FALSE            FALSE
## 11  1.916667     11.839323   FALSE FALSE    FALSE            FALSE
## 6   3.431034      3.382664   FALSE FALSE    FALSE            FALSE
## 9   2.238095      0.845666   FALSE FALSE    FALSE            FALSE
## 10  2.238095      0.845666   FALSE FALSE    FALSE            FALSE
#subset(glb_feats_df, id %in% c("A.nuppr.log", "S.nuppr.log"))
print(myplot_scatter(glb_feats_df, "percentUnique", "freqRatio", 
                     colorcol_name="myNearZV", jitter=TRUE) + 
          geom_point(aes(shape=nzv)) + xlim(-5, 25))
## Warning in myplot_scatter(glb_feats_df, "percentUnique", "freqRatio",
## colorcol_name = "myNearZV", : converting myNearZV to class:factor
## Warning: Removed 2 rows containing missing values (geom_point).
## Warning: Removed 2 rows containing missing values (geom_point).
## Warning: Removed 2 rows containing missing values (geom_point).

print(subset(glb_feats_df, myNearZV))
##  [1] id               cor.y            exclude.as.feat  cor.y.abs       
##  [5] cor.high.X       freqRatio        percentUnique    zeroVar         
##  [9] nzv              myNearZV         is.cor.y.abs.low
## <0 rows> (or 0-length row.names)
glb_allobs_df <- glb_allobs_df[, setdiff(names(glb_allobs_df), 
                                         subset(glb_feats_df, myNearZV)$id)]

if (!is.null(glb_interaction_only_features))
    glb_feats_df[glb_feats_df$id %in% glb_interaction_only_features, "interaction.feat"] <-
        names(glb_interaction_only_features) else
    glb_feats_df$interaction.feat <- NA        

mycheck_problem_data(glb_allobs_df, terminate = TRUE)
## [1] "numeric data missing in : "
## named integer(0)
## [1] "numeric data w/ 0s in : "
##              male       time.served multiple.offenses          violator 
##               130                 1               313               597 
## [1] "numeric data w/ Infs in : "
## named integer(0)
## [1] "numeric data w/ NaNs in : "
## named integer(0)
## [1] "string data missing in : "
## .rownames 
##         0
# glb_allobs_df %>% filter(is.na(Married.fctr)) %>% tbl_df()
# glb_allobs_df %>% count(Married.fctr)
# levels(glb_allobs_df$Married.fctr)

glb_chunks_df <- myadd_chunk(glb_chunks_df, "partition.data.training", major.inc=TRUE)
##                     label step_major step_minor    bgn    end elapsed
## 8         select.features          5          0 23.158 23.765   0.608
## 9 partition.data.training          6          0 23.766     NA      NA

Step 6.0: partition data training

if (all(is.na(glb_newobs_df[, glb_rsp_var]))) {
    require(caTools)
    
    set.seed(glb_split_sample.seed)
    split <- sample.split(glb_trnobs_df[, glb_rsp_var_raw], 
        SplitRatio=1 - (nrow(glb_newobs_df) * 1.1 / nrow(glb_trnobs_df)))
    glb_fitobs_df <- glb_trnobs_df[split, ] 
    glb_OOBobs_df <- glb_trnobs_df[!split ,]    
} else {
    print(sprintf("Newdata contains non-NA data for %s; setting OOB to Newdata", 
                  glb_rsp_var))
    glb_fitobs_df <- glb_trnobs_df; glb_OOBobs_df <- glb_newobs_df
}
## [1] "Newdata contains non-NA data for violator.fctr; setting OOB to Newdata"
if (!is.null(glb_max_fitobs) && (nrow(glb_fitobs_df) > glb_max_fitobs)) {
    warning("glb_fitobs_df restricted to glb_max_fitobs: ", 
            format(glb_max_fitobs, big.mark=","))
    org_fitobs_df <- glb_fitobs_df
    glb_fitobs_df <- 
        org_fitobs_df[split <- sample.split(org_fitobs_df[, glb_rsp_var_raw], 
                                            SplitRatio=glb_max_fitobs), ]
    org_fitobs_df <- NULL
}

glb_allobs_df$.lcn <- ""
glb_allobs_df[glb_allobs_df[, glb_id_var] %in% 
              glb_fitobs_df[, glb_id_var], ".lcn"] <- "Fit"
glb_allobs_df[glb_allobs_df[, glb_id_var] %in% 
              glb_OOBobs_df[, glb_id_var], ".lcn"] <- "OOB"

dsp_class_dstrb <- function(obs_df, location_var, partition_var) {
    xtab_df <- mycreate_xtab_df(obs_df, c(location_var, partition_var))
    rownames(xtab_df) <- xtab_df[, location_var]
    xtab_df <- xtab_df[, -grepl(location_var, names(xtab_df))]
    print(xtab_df)
    print(xtab_df / rowSums(xtab_df, na.rm=TRUE))    
}    

# Ensure proper splits by glb_rsp_var_raw & user-specified feature for OOB vs. new
if (!is.null(glb_category_vars)) {
    if (glb_is_classification)
        dsp_class_dstrb(glb_allobs_df, ".lcn", glb_rsp_var_raw)
    newobs_ctgry_df <- mycreate_sqlxtab_df(subset(glb_allobs_df, .src == "Test"), 
                                           glb_category_vars)
    OOBobs_ctgry_df <- mycreate_sqlxtab_df(subset(glb_allobs_df, .lcn == "OOB"), 
                                           glb_category_vars)
    glb_ctgry_df <- merge(newobs_ctgry_df, OOBobs_ctgry_df, by=glb_category_vars
                          , all=TRUE, suffixes=c(".Tst", ".OOB"))
    glb_ctgry_df$.freqRatio.Tst <- glb_ctgry_df$.n.Tst / sum(glb_ctgry_df$.n.Tst, na.rm=TRUE)
    glb_ctgry_df$.freqRatio.OOB <- glb_ctgry_df$.n.OOB / sum(glb_ctgry_df$.n.OOB, na.rm=TRUE)
    print(orderBy(~-.freqRatio.Tst-.freqRatio.OOB, glb_ctgry_df))
}

# Run this line by line
print("glb_feats_df:");   print(dim(glb_feats_df))
## [1] "glb_feats_df:"
## [1] 12 12
sav_feats_df <- glb_feats_df
glb_feats_df <- sav_feats_df

glb_feats_df[, "rsp_var_raw"] <- FALSE
glb_feats_df[glb_feats_df$id == glb_rsp_var_raw, "rsp_var_raw"] <- TRUE 
glb_feats_df$exclude.as.feat <- (glb_feats_df$exclude.as.feat == 1)
if (!is.null(glb_id_var) && glb_id_var != ".rownames")
    glb_feats_df[glb_feats_df$id %in% glb_id_var, "id_var"] <- TRUE 
add_feats_df <- data.frame(id=glb_rsp_var, exclude.as.feat=TRUE, rsp_var=TRUE)
row.names(add_feats_df) <- add_feats_df$id; print(add_feats_df)
##                          id exclude.as.feat rsp_var
## violator.fctr violator.fctr            TRUE    TRUE
glb_feats_df <- myrbind_df(glb_feats_df, add_feats_df)
if (glb_id_var != ".rownames")
    print(subset(glb_feats_df, rsp_var_raw | rsp_var | id_var)) else
    print(subset(glb_feats_df, rsp_var_raw | rsp_var))    
##                          id cor.y exclude.as.feat cor.y.abs cor.high.X
## 12                 violator     1            TRUE         1         NA
## violator.fctr violator.fctr    NA            TRUE        NA         NA
##               freqRatio percentUnique zeroVar   nzv myNearZV
## 12                  7.6      0.422833   FALSE FALSE    FALSE
## violator.fctr        NA            NA      NA    NA       NA
##               is.cor.y.abs.low interaction.feat rsp_var_raw rsp_var
## 12                       FALSE               NA        TRUE      NA
## violator.fctr               NA               NA          NA    TRUE
print("glb_feats_df vs. glb_allobs_df: "); 
## [1] "glb_feats_df vs. glb_allobs_df: "
print(setdiff(glb_feats_df$id, names(glb_allobs_df)))
## character(0)
print("glb_allobs_df vs. glb_feats_df: "); 
## [1] "glb_allobs_df vs. glb_feats_df: "
# Ensure these are only chr vars
print(setdiff(setdiff(names(glb_allobs_df), glb_feats_df$id), 
                myfind_chr_cols_df(glb_allobs_df)))
## character(0)
#print(setdiff(setdiff(names(glb_allobs_df), glb_exclude_vars_as_features), 
#                glb_feats_df$id))

print("glb_allobs_df: "); print(dim(glb_allobs_df))
## [1] "glb_allobs_df: "
## [1] 675  16
print("glb_trnobs_df: "); print(dim(glb_trnobs_df))
## [1] "glb_trnobs_df: "
## [1] 473  15
print("glb_fitobs_df: "); print(dim(glb_fitobs_df))
## [1] "glb_fitobs_df: "
## [1] 473  15
print("glb_OOBobs_df: "); print(dim(glb_OOBobs_df))
## [1] "glb_OOBobs_df: "
## [1] 202  15
print("glb_newobs_df: "); print(dim(glb_newobs_df))
## [1] "glb_newobs_df: "
## [1] 202  15
# # Does not handle NULL or length(glb_id_var) > 1
# glb_allobs_df$.src.trn <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_trnobs_df[, glb_id_var], 
#                 ".src.trn"] <- 1 
# glb_allobs_df$.src.fit <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_fitobs_df[, glb_id_var], 
#                 ".src.fit"] <- 1 
# glb_allobs_df$.src.OOB <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_OOBobs_df[, glb_id_var], 
#                 ".src.OOB"] <- 1 
# glb_allobs_df$.src.new <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_newobs_df[, glb_id_var], 
#                 ".src.new"] <- 1 
# #print(unique(glb_allobs_df[, ".src.trn"]))
# write_cols <- c(glb_feats_df$id, 
#                 ".src.trn", ".src.fit", ".src.OOB", ".src.new")
# glb_allobs_df <- glb_allobs_df[, write_cols]
# 
# tmp_feats_df <- glb_feats_df
# tmp_entity_df <- glb_allobs_df

if (glb_save_envir)
    save(glb_feats_df, 
         glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
         file=paste0(glb_out_pfx, "blddfs_dsk.RData"))
# load(paste0(glb_out_pfx, "blddfs_dsk.RData"))

# if (!all.equal(tmp_feats_df, glb_feats_df))
#     stop("glb_feats_df r/w not working")
# if (!all.equal(tmp_entity_df, glb_allobs_df))
#     stop("glb_allobs_df r/w not working")

rm(split)

glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=TRUE)
##                      label step_major step_minor    bgn    end elapsed
## 9  partition.data.training          6          0 23.766 24.088   0.322
## 10              fit.models          7          0 24.088     NA      NA

Step 7.0: fit models

# load(paste0(glb_out_pfx, "dsk.RData"))
# keep_cols <- setdiff(names(glb_allobs_df), 
#                      grep("^.src", names(glb_allobs_df), value=TRUE))
# glb_trnobs_df <- glb_allobs_df[glb_allobs_df$.src.trn == 1, keep_cols]
# glb_fitobs_df <- glb_allobs_df[glb_allobs_df$.src.fit == 1, keep_cols]
# glb_OOBobs_df <- glb_allobs_df[glb_allobs_df$.src.OOB == 1, keep_cols]
# glb_newobs_df <- glb_allobs_df[glb_allobs_df$.src.new == 1, keep_cols]
# 
# glb_models_lst <- list(); glb_models_df <- data.frame()
# 
if (glb_is_classification && glb_is_binomial && 
        (length(unique(glb_fitobs_df[, glb_rsp_var])) < 2))
    stop("glb_fitobs_df$", glb_rsp_var, ": contains less than 2 unique values: ",
         paste0(unique(glb_fitobs_df[, glb_rsp_var]), collapse=", "))

max_cor_y_x_vars <- orderBy(~ -cor.y.abs, 
        subset(glb_feats_df, (exclude.as.feat == 0) & !is.cor.y.abs.low & 
                                is.na(cor.high.X)))[1:2, "id"]
# while(length(max_cor_y_x_vars) < 2) {
#     max_cor_y_x_vars <- c(max_cor_y_x_vars, orderBy(~ -cor.y.abs, 
#             subset(glb_feats_df, (exclude.as.feat == 0) & !is.cor.y.abs.low))[3, "id"])    
# }
if (!is.null(glb_Baseline_mdl_var)) {
    if ((max_cor_y_x_vars[1] != glb_Baseline_mdl_var) & 
        (glb_feats_df[glb_feats_df$id == max_cor_y_x_vars[1], "cor.y.abs"] > 
         glb_feats_df[glb_feats_df$id == glb_Baseline_mdl_var, "cor.y.abs"]))
        stop(max_cor_y_x_vars[1], " has a higher correlation with ", glb_rsp_var, 
             " than the Baseline var: ", glb_Baseline_mdl_var)
}

glb_model_type <- ifelse(glb_is_regression, "regression", "classification")
    
# Baseline
if (!is.null(glb_Baseline_mdl_var)) 
    ret_lst <- myfit_mdl(model_id="Baseline", 
                         model_method="mybaseln_classfr",
                        indep_vars_vctr=glb_Baseline_mdl_var,
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)

# Most Frequent Outcome "MFO" model: mean(y) for regression
#   Not using caret's nullModel since model stats not avl
#   Cannot use rpart for multinomial classification since it predicts non-MFO
ret_lst <- myfit_mdl(model_id="MFO", 
                     model_method=ifelse(glb_is_regression, "lm", "myMFO_classfr"), 
                     model_type=glb_model_type,
                        indep_vars_vctr=".rnorm",
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)
## [1] "fitting model: MFO.myMFO_classfr"
## [1] "    indep_vars: .rnorm"
## Fitting parameter = none on full training set
## [1] "in MFO.Classifier$fit"
## [1] "unique.vals:"
## [1] N Y
## Levels: N Y
## [1] "unique.prob:"
## y
##         N         Y 
## 0.8837209 0.1162791 
## [1] "MFO.val:"
## [1] "N"
##             Length Class      Mode     
## unique.vals 2      factor     numeric  
## unique.prob 2      -none-     numeric  
## MFO.val     1      -none-     character
## x.names     1      -none-     character
## xNames      1      -none-     character
## problemType 1      -none-     character
## tuneValue   1      data.frame list     
## obsLevels   2      -none-     character
## [1] "    calling mypredict_mdl for fit:"
## Loading required package: ROCR
## Loading required package: gplots
## 
## Attaching package: 'gplots'
## 
## The following object is masked from 'package:stats':
## 
##     lowess
## [1] "in MFO.Classifier$prob"
##           N         Y
## 1 0.8837209 0.1162791
## 2 0.8837209 0.1162791
## 3 0.8837209 0.1162791
## 4 0.8837209 0.1162791
## 5 0.8837209 0.1162791
## 6 0.8837209 0.1162791
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.MFO.myMFO_classfr.N
## 1             N                                       418
## 2             Y                                        55
##          Prediction
## Reference   N   Y
##         N 418   0
##         Y  55   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.837209e-01   0.000000e+00   8.513472e-01   9.111909e-01   8.837209e-01 
## AccuracyPValue  McnemarPValue 
##   5.358475e-01   3.304751e-13 
## [1] "    calling mypredict_mdl for OOB:"
## [1] "in MFO.Classifier$prob"
##           N         Y
## 1 0.8837209 0.1162791
## 2 0.8837209 0.1162791
## 3 0.8837209 0.1162791
## 4 0.8837209 0.1162791
## 5 0.8837209 0.1162791
## 6 0.8837209 0.1162791
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.MFO.myMFO_classfr.N
## 1             N                                       179
## 2             Y                                        23
##          Prediction
## Reference   N   Y
##         N 179   0
##         Y  23   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.861386e-01   0.000000e+00   8.340624e-01   9.264369e-01   8.861386e-01 
## AccuracyPValue  McnemarPValue 
##   5.552509e-01   4.489784e-06 
##            model_id  model_method  feats max.nTuningRuns
## 1 MFO.myMFO_classfr myMFO_classfr .rnorm               0
##   min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1                      0.407                 0.003         0.5
##   opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1                    0.5               0        0.8837209
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8513472             0.9111909             0         0.5
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.5               0        0.8861386
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1             0.8340624             0.9264369             0
if (glb_is_classification)
    # "random" model - only for classification; 
    #   none needed for regression since it is same as MFO
    ret_lst <- myfit_mdl(model_id="Random", model_method="myrandom_classfr",
                            model_type=glb_model_type,                         
                            indep_vars_vctr=".rnorm",
                            rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                            fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)
## [1] "fitting model: Random.myrandom_classfr"
## [1] "    indep_vars: .rnorm"
## Fitting parameter = none on full training set
##             Length Class      Mode     
## unique.vals 2      factor     numeric  
## unique.prob 2      table      numeric  
## xNames      1      -none-     character
## problemType 1      -none-     character
## tuneValue   1      data.frame list     
## obsLevels   2      -none-     character
## [1] "    calling mypredict_mdl for fit:"
## [1] "in Random.Classifier$prob"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.2083333
## 3        0.2 0.1523810
## 4        0.3 0.1523810
## 5        0.4 0.1523810
## 6        0.5 0.1523810
## 7        0.6 0.1523810
## 8        0.7 0.1523810
## 9        0.8 0.1523810
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.1000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Random.myrandom_classfr.Y
## 1             N                                             418
## 2             Y                                              55
##          Prediction
## Reference   N   Y
##         N   0 418
##         Y   0  55
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   1.162791e-01   0.000000e+00   8.880912e-02   1.486528e-01   8.837209e-01 
## AccuracyPValue  McnemarPValue 
##   1.000000e+00   1.809600e-92 
## [1] "    calling mypredict_mdl for OOB:"
## [1] "in Random.Classifier$prob"

##    threshold    f.score
## 1        0.0 0.20444444
## 2        0.1 0.20444444
## 3        0.2 0.04347826
## 4        0.3 0.04347826
## 5        0.4 0.04347826
## 6        0.5 0.04347826
## 7        0.6 0.04347826
## 8        0.7 0.04347826
## 9        0.8 0.04347826
## 10       0.9 0.00000000
## 11       1.0 0.00000000

## [1] "Classifier Probability Threshold: 0.1000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Random.myrandom_classfr.Y
## 1             N                                             179
## 2             Y                                              23
##          Prediction
## Reference   N   Y
##         N   0 179
##         Y   0  23
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   1.138614e-01   0.000000e+00   7.356311e-02   1.659376e-01   8.861386e-01 
## AccuracyPValue  McnemarPValue 
##   1.000000e+00   2.183997e-40 
##                  model_id     model_method  feats max.nTuningRuns
## 1 Random.myrandom_classfr myrandom_classfr .rnorm               0
##   min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1                      0.231                 0.001    0.522488
##   opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1                    0.1       0.2083333        0.1162791
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1            0.08880912             0.1486528             0   0.4602866
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.1       0.2044444        0.1138614
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1            0.07356311             0.1659376             0
# Any models that have tuning parameters has "better" results with cross-validation
#   (except rf) & "different" results for different outcome metrics

# Max.cor.Y
#   Check impact of cv
#       rpart is not a good candidate since caret does not optimize cp (only tuning parameter of rpart) well
ret_lst <- myfit_mdl(model_id="Max.cor.Y.cv.0", 
                        model_method="rpart",
                     model_type=glb_model_type,
                        indep_vars_vctr=max_cor_y_x_vars,
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)
## [1] "fitting model: Max.cor.Y.cv.0.rpart"
## [1] "    indep_vars: state.fctr, max.sentence"
## Loading required package: rpart
## Fitting cp = 0.0182 on full training set
## Loading required package: rpart.plot

## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7, 
##     cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, 
##     surrogatestyle = 0, maxdepth = 30, xval = 0))
##   n= 473 
## 
##           CP nsplit rel error
## 1 0.01818182      0         1
## 
## Node number 1: 473 observations
##   predicted class=N  expected loss=0.1162791  P(node) =1
##     class counts:   418    55
##    probabilities: 0.884 0.116 
## 
## n= 473 
## 
## node), split, n, loss, yval, (yprob)
##       * denotes terminal node
## 
## 1) root 473 55 N (0.8837209 0.1162791) *
## [1] "    calling mypredict_mdl for fit:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Max.cor.Y.cv.0.rpart.N
## 1             N                                          418
## 2             Y                                           55
##          Prediction
## Reference   N   Y
##         N 418   0
##         Y  55   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.837209e-01   0.000000e+00   8.513472e-01   9.111909e-01   8.837209e-01 
## AccuracyPValue  McnemarPValue 
##   5.358475e-01   3.304751e-13 
## [1] "    calling mypredict_mdl for OOB:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Max.cor.Y.cv.0.rpart.N
## 1             N                                          179
## 2             Y                                           23
##          Prediction
## Reference   N   Y
##         N 179   0
##         Y  23   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.861386e-01   0.000000e+00   8.340624e-01   9.264369e-01   8.861386e-01 
## AccuracyPValue  McnemarPValue 
##   5.552509e-01   4.489784e-06 
##               model_id model_method                    feats
## 1 Max.cor.Y.cv.0.rpart        rpart state.fctr, max.sentence
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               0                       0.62                  0.01
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1         0.5                    0.5               0        0.8837209
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8513472             0.9111909             0         0.5
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.5               0        0.8861386
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1             0.8340624             0.9264369             0
ret_lst <- myfit_mdl(model_id="Max.cor.Y.cv.0.cp.0", 
                        model_method="rpart",
                     model_type=glb_model_type,
                        indep_vars_vctr=max_cor_y_x_vars,
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                        n_cv_folds=0, 
            tune_models_df=data.frame(parameter="cp", min=0.0, max=0.0, by=0.1))
## [1] "fitting model: Max.cor.Y.cv.0.cp.0.rpart"
## [1] "    indep_vars: state.fctr, max.sentence"
## Fitting cp = 0 on full training set

## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7, 
##     cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, 
##     surrogatestyle = 0, maxdepth = 30, xval = 0))
##   n= 473 
## 
##           CP nsplit rel error
## 1 0.01818182      0 1.0000000
## 2 0.00000000      2 0.9636364
## 
## Variable importance
##  state.fctr3 max.sentence 
##           71           29 
## 
## Node number 1: 473 observations,    complexity param=0.01818182
##   predicted class=N  expected loss=0.1162791  P(node) =1
##     class counts:   418    55
##    probabilities: 0.884 0.116 
##   left son=2 (425 obs) right son=3 (48 obs)
##   Primary splits:
##       state.fctr3  < 0.5  to the left,  improve=11.0243000, (0 missing)
##       state.fctr4  < 0.5  to the right, improve= 7.6921560, (0 missing)
##       max.sentence < 12.5 to the right, improve= 2.0817270, (0 missing)
##       state.fctr2  < 0.5  to the left,  improve= 0.1284655, (0 missing)
##   Surrogate splits:
##       max.sentence < 7    to the right, agree=0.93, adj=0.313, (0 split)
## 
## Node number 2: 425 observations
##   predicted class=N  expected loss=0.08  P(node) =0.8985201
##     class counts:   391    34
##    probabilities: 0.920 0.080 
## 
## Node number 3: 48 observations,    complexity param=0.01818182
##   predicted class=N  expected loss=0.4375  P(node) =0.1014799
##     class counts:    27    21
##    probabilities: 0.562 0.438 
##   left son=6 (24 obs) right son=7 (24 obs)
##   Primary splits:
##       max.sentence < 9.5  to the left,  improve=1.041667, (0 missing)
## 
## Node number 6: 24 observations
##   predicted class=N  expected loss=0.3333333  P(node) =0.05073996
##     class counts:    16     8
##    probabilities: 0.667 0.333 
## 
## Node number 7: 24 observations
##   predicted class=Y  expected loss=0.4583333  P(node) =0.05073996
##     class counts:    11    13
##    probabilities: 0.458 0.542 
## 
## n= 473 
## 
## node), split, n, loss, yval, (yprob)
##       * denotes terminal node
## 
## 1) root 473 55 N (0.8837209 0.1162791)  
##   2) state.fctr3< 0.5 425 34 N (0.9200000 0.0800000) *
##   3) state.fctr3>=0.5 48 21 N (0.5625000 0.4375000)  
##     6) max.sentence< 9.5 24  8 N (0.6666667 0.3333333) *
##     7) max.sentence>=9.5 24 11 Y (0.4583333 0.5416667) *
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.4077670
## 3        0.2 0.4077670
## 4        0.3 0.4077670
## 5        0.4 0.3291139
## 6        0.5 0.3291139
## 7        0.6 0.0000000
## 8        0.7 0.0000000
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.3000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.N
## 1             N                                               391
## 2             Y                                                34
##   violator.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.Y
## 1                                                27
## 2                                                21
##          Prediction
## Reference   N   Y
##         N 391  27
##         Y  34  21
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##      0.8710359      0.3357812      0.8374414      0.8998980      0.8837209 
## AccuracyPValue  McnemarPValue 
##      0.8251302      0.4423557 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold   f.score
## 1        0.0 0.2044444
## 2        0.1 0.5614035
## 3        0.2 0.5614035
## 4        0.3 0.5614035
## 5        0.4 0.3243243
## 6        0.5 0.3243243
## 7        0.6 0.0000000
## 8        0.7 0.0000000
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.3000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.N
## 1             N                                               161
## 2             Y                                                 7
##   violator.fctr.predict.Max.cor.Y.cv.0.cp.0.rpart.Y
## 1                                                18
## 2                                                16
##          Prediction
## Reference   N   Y
##         N 161  18
##         Y   7  16
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##     0.87623762     0.49246231     0.82274322     0.91828207     0.88613861 
## AccuracyPValue  McnemarPValue 
##     0.71681786     0.04550026 
##                    model_id model_method                    feats
## 1 Max.cor.Y.cv.0.cp.0.rpart        rpart state.fctr, max.sentence
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               0                      0.448                 0.007
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1   0.6612223                    0.3        0.407767        0.8710359
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8374414              0.899898     0.3357812   0.7951178
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.3       0.5614035        0.8762376
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1             0.8227432             0.9182821     0.4924623
if (glb_is_regression || glb_is_binomial) # For multinomials this model will be run next by default
ret_lst <- myfit_mdl(model_id="Max.cor.Y", 
                        model_method="rpart",
                     model_type=glb_model_type,
                        indep_vars_vctr=max_cor_y_x_vars,
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                        n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
## [1] "fitting model: Max.cor.Y.rpart"
## [1] "    indep_vars: state.fctr, max.sentence"
## Aggregating results
## Selecting tuning parameters
## Fitting cp = 0.0182 on full training set
## Warning in myfit_mdl(model_id = "Max.cor.Y", model_method = "rpart",
## model_type = glb_model_type, : model's bestTune found at an extreme of
## tuneGrid for parameter: cp

## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7, 
##     cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, 
##     surrogatestyle = 0, maxdepth = 30, xval = 0))
##   n= 473 
## 
##           CP nsplit rel error
## 1 0.01818182      0         1
## 
## Node number 1: 473 observations
##   predicted class=N  expected loss=0.1162791  P(node) =1
##     class counts:   418    55
##    probabilities: 0.884 0.116 
## 
## n= 473 
## 
## node), split, n, loss, yval, (yprob)
##       * denotes terminal node
## 
## 1) root 473 55 N (0.8837209 0.1162791) *
## [1] "    calling mypredict_mdl for fit:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Max.cor.Y.rpart.N
## 1             N                                     418
## 2             Y                                      55
##          Prediction
## Reference   N   Y
##         N 418   0
##         Y  55   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.837209e-01   0.000000e+00   8.513472e-01   9.111909e-01   8.837209e-01 
## AccuracyPValue  McnemarPValue 
##   5.358475e-01   3.304751e-13 
## [1] "    calling mypredict_mdl for OOB:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Max.cor.Y.rpart.N
## 1             N                                     179
## 2             Y                                      23
##          Prediction
## Reference   N   Y
##         N 179   0
##         Y  23   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.861386e-01   0.000000e+00   8.340624e-01   9.264369e-01   8.861386e-01 
## AccuracyPValue  McnemarPValue 
##   5.552509e-01   4.489784e-06 
##          model_id model_method                    feats max.nTuningRuns
## 1 Max.cor.Y.rpart        rpart state.fctr, max.sentence               3
##   min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1                      0.997                  0.01         0.5
##   opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1                    0.5               0        0.8773953
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8513472             0.9111909     0.1504134         0.5
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.5               0        0.8861386
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1             0.8340624             0.9264369             0
##   max.AccuracySD.fit max.KappaSD.fit
## 1         0.01441156       0.1336443
# Used to compare vs. Interactions.High.cor.Y and/or Max.cor.Y.TmSrs
ret_lst <- myfit_mdl(model_id="Max.cor.Y", 
                        model_method=ifelse(glb_is_regression, "lm", 
                                        ifelse(glb_is_binomial, "glm", "rpart")),
                     model_type=glb_model_type,
                        indep_vars_vctr=max_cor_y_x_vars,
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                        n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
## [1] "fitting model: Max.cor.Y.glm"
## [1] "    indep_vars: state.fctr, max.sentence"
## Aggregating results
## Fitting final model on full training set

## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.3150  -0.5430  -0.2339  -0.2188   2.7122  
## 
## Coefficients:
##              Estimate Std. Error z value Pr(>|z|)    
## (Intercept)  -2.63225    0.72492  -3.631 0.000282 ***
## state.fctr2  -0.01720    0.41845  -0.041 0.967208    
## state.fctr3   1.73555    0.44936   3.862 0.000112 ***
## state.fctr4  -1.96485    0.49575  -3.963 7.39e-05 ***
## max.sentence  0.06747    0.04860   1.388 0.165058    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 278.54  on 468  degrees of freedom
## AIC: 288.54
## 
## Number of Fisher Scoring iterations: 6
## 
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.3356164
## 3        0.2 0.4077670
## 4        0.3 0.4077670
## 5        0.4 0.3678161
## 6        0.5 0.1290323
## 7        0.6 0.0000000
## 8        0.7 0.0000000
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.3000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Max.cor.Y.glm.N
## 1             N                                   391
## 2             Y                                    34
##   violator.fctr.predict.Max.cor.Y.glm.Y
## 1                                    27
## 2                                    21
##          Prediction
## Reference   N   Y
##         N 391  27
##         Y  34  21
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##      0.8710359      0.3357812      0.8374414      0.8998980      0.8837209 
## AccuracyPValue  McnemarPValue 
##      0.8251302      0.4423557 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold   f.score
## 1        0.0 0.2044444
## 2        0.1 0.3437500
## 3        0.2 0.5614035
## 4        0.3 0.5614035
## 5        0.4 0.4090909
## 6        0.5 0.2222222
## 7        0.6 0.0000000
## 8        0.7 0.0000000
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.3000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Max.cor.Y.glm.N
## 1             N                                   161
## 2             Y                                     7
##   violator.fctr.predict.Max.cor.Y.glm.Y
## 1                                    18
## 2                                    16
##          Prediction
## Reference   N   Y
##         N 161  18
##         Y   7  16
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##     0.87623762     0.49246231     0.82274322     0.91828207     0.88613861 
## AccuracyPValue  McnemarPValue 
##     0.71681786     0.04550026 
##        model_id model_method                    feats max.nTuningRuns
## 1 Max.cor.Y.glm          glm state.fctr, max.sentence               1
##   min.elapsedtime.everything min.elapsedtime.final max.auc.fit
## 1                      0.884                 0.011   0.8018486
##   opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1                    0.3        0.407767         0.879505
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8374414              0.899898     0.1380265   0.8581491
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.3       0.5614035        0.8762376
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1             0.8227432             0.9182821     0.4924623    288.5369
##   max.AccuracySD.fit max.KappaSD.fit
## 1        0.005969975       0.1210085
if (!is.null(glb_date_vars) && 
    (sum(grepl(paste(glb_date_vars, "\\.day\\.minutes\\.poly\\.", sep=""),
               names(glb_allobs_df))) > 0)) {
# ret_lst <- myfit_mdl(model_id="Max.cor.Y.TmSrs.poly1", 
#                         model_method=ifelse(glb_is_regression, "lm", 
#                                         ifelse(glb_is_binomial, "glm", "rpart")),
#                      model_type=glb_model_type,
#                         indep_vars_vctr=c(max_cor_y_x_vars, paste0(glb_date_vars, ".day.minutes")),
#                         rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
#                         fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
#                         n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
# 
ret_lst <- myfit_mdl(model_id="Max.cor.Y.TmSrs.poly", 
                        model_method=ifelse(glb_is_regression, "lm", 
                                        ifelse(glb_is_binomial, "glm", "rpart")),
                     model_type=glb_model_type,
                        indep_vars_vctr=c(max_cor_y_x_vars, 
            grep(paste(glb_date_vars, "\\.day\\.minutes\\.poly\\.", sep=""),
                        names(glb_allobs_df), value=TRUE)),
                        rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                        n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
}

# Interactions.High.cor.Y
if (length(int_feats <- setdiff(unique(glb_feats_df$cor.high.X), NA)) > 0) {
    # lm & glm handle interaction terms; rpart & rf do not
    if (glb_is_regression || glb_is_binomial) {
        indep_vars_vctr <- 
            c(max_cor_y_x_vars, paste(max_cor_y_x_vars[1], int_feats, sep=":"))            
    } else { indep_vars_vctr <- union(max_cor_y_x_vars, int_feats) }
    
    ret_lst <- myfit_mdl(model_id="Interact.High.cor.Y", 
                            model_method=ifelse(glb_is_regression, "lm", 
                                        ifelse(glb_is_binomial, "glm", "rpart")),
                         model_type=glb_model_type,
                            indep_vars_vctr,
                            glb_rsp_var, glb_rsp_var_out,
                            fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                            n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)                        
}    

# Low.cor.X
# if (glb_is_classification && glb_is_binomial)
#     indep_vars_vctr <- subset(glb_feats_df, is.na(cor.high.X) & 
#                                             is.ConditionalX.y & 
#                                             (exclude.as.feat != 1))[, "id"] else
indep_vars_vctr <- subset(glb_feats_df, is.na(cor.high.X) & !myNearZV & 
                              (exclude.as.feat != 1))[, "id"]  
myadjust_interaction_feats <- function(vars_vctr) {
    for (feat in subset(glb_feats_df, !is.na(interaction.feat))$id)
        if (feat %in% vars_vctr)
            vars_vctr <- union(setdiff(vars_vctr, feat), 
                paste0(glb_feats_df[glb_feats_df$id == feat, "interaction.feat"], ":", feat))
    return(vars_vctr)
}
indep_vars_vctr <- myadjust_interaction_feats(indep_vars_vctr)
ret_lst <- myfit_mdl(model_id="Low.cor.X", 
                        model_method=ifelse(glb_is_regression, "lm", 
                                        ifelse(glb_is_binomial, "glm", "rpart")),
                        indep_vars_vctr=indep_vars_vctr,
                        model_type=glb_model_type,                     
                        glb_rsp_var, glb_rsp_var_out,
                        fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                        n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
## [1] "fitting model: Low.cor.X.glm"
## [1] "    indep_vars: multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr"
## Aggregating results
## Fitting final model on full training set

## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.7256  -0.4288  -0.2719  -0.1681   2.8478  
## 
## Coefficients:
##                     Estimate Std. Error z value Pr(>|z|)    
## (Intercept)       -4.2474963  1.2952911  -3.279  0.00104 ** 
## multiple.offenses  1.6254434  0.3886164   4.183 2.88e-05 ***
## race               0.8823506  0.3953679   2.232  0.02563 *  
## age               -0.0003604  0.0160915  -0.022  0.98213    
## male               0.3878796  0.4385200   0.885  0.37642    
## .rnorm             0.0474484  0.1748880   0.271  0.78615    
## crime.fctr2        0.6720975  0.5030137   1.336  0.18150    
## crime.fctr3       -0.2805264  0.4328933  -0.648  0.51697    
## crime.fctr4       -0.0036558  0.5717918  -0.006  0.99490    
## time.served       -0.1219743  0.1205154  -1.012  0.31149    
## max.sentence       0.0801944  0.0554146   1.447  0.14785    
## state.fctr2        0.4585050  0.4855775   0.944  0.34504    
## state.fctr3        0.8535218  0.5607749   1.522  0.12800    
## state.fctr4       -3.3945448  0.6115599  -5.551 2.85e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 251.41  on 459  degrees of freedom
## AIC: 279.41
## 
## Number of Fisher Scoring iterations: 6
## 
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.4081633
## 3        0.2 0.4822695
## 4        0.3 0.4705882
## 5        0.4 0.4565217
## 6        0.5 0.4102564
## 7        0.6 0.2941176
## 8        0.7 0.2187500
## 9        0.8 0.1034483
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.2000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Low.cor.X.glm.N
## 1             N                                   366
## 2             Y                                    21
##   violator.fctr.predict.Low.cor.X.glm.Y
## 1                                    52
## 2                                    34
##          Prediction
## Reference   N   Y
##         N 366  52
##         Y  21  34
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   0.8456659619   0.3966942149   0.8099028745   0.8770336126   0.8837209302 
## AccuracyPValue  McnemarPValue 
##   0.9947311468   0.0004460309 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold    f.score
## 1        0.0 0.20444444
## 2        0.1 0.43010753
## 3        0.2 0.52307692
## 4        0.3 0.50909091
## 5        0.4 0.52000000
## 6        0.5 0.54166667
## 7        0.6 0.25806452
## 8        0.7 0.20689655
## 9        0.8 0.22222222
## 10       0.9 0.08333333
## 11       1.0 0.00000000

## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Low.cor.X.glm.N
## 1             N                                   167
## 2             Y                                    10
##   violator.fctr.predict.Low.cor.X.glm.Y
## 1                                    12
## 2                                    13
##          Prediction
## Reference   N   Y
##         N 167  12
##         Y  10  13
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##      0.8910891      0.4799906      0.8397588      0.9304755      0.8861386 
## AccuracyPValue  McnemarPValue 
##      0.4672071      0.8311704 
##        model_id model_method
## 1 Low.cor.X.glm          glm
##                                                                                           feats
## 1 multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               1                       1.14                 0.012
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1    0.845759                    0.2       0.4822695         0.879505
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8099029             0.8770336     0.2015256   0.8938547
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.5       0.5416667        0.8910891
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1             0.8397588             0.9304755     0.4799906    279.4111
##   max.AccuracySD.fit max.KappaSD.fit
## 1        0.005969975      0.07399248
rm(ret_lst)

glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)
##         label step_major step_minor    bgn    end elapsed
## 10 fit.models          7          0 24.088 41.151  17.063
## 11 fit.models          7          1 41.151     NA      NA
fit.models_1_chunk_df <- myadd_chunk(NULL, "fit.models_1_bgn")
##              label step_major step_minor    bgn end elapsed
## 1 fit.models_1_bgn          1          0 43.434  NA      NA
# Options:
#   1. rpart & rf manual tuning
#   2. rf without pca (default: with pca)

#stop(here); sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df
#glb_models_lst <- sav_models_lst; glb_models_df <- sav_models_df

# All X that is not user excluded
# if (glb_is_classification && glb_is_binomial) {
#     model_id_pfx <- "Conditional.X"
# # indep_vars_vctr <- setdiff(names(glb_fitobs_df), union(glb_rsp_var, glb_exclude_vars_as_features))
#     indep_vars_vctr <- subset(glb_feats_df, is.ConditionalX.y & 
#                                             (exclude.as.feat != 1))[, "id"]
# } else {
    model_id_pfx <- "All.X"
    indep_vars_vctr <- subset(glb_feats_df, !myNearZV &
                                            (exclude.as.feat != 1))[, "id"]
# }

indep_vars_vctr <- myadjust_interaction_feats(indep_vars_vctr)

for (method in glb_models_method_vctr) {
    fit.models_1_chunk_df <- myadd_chunk(fit.models_1_chunk_df, 
                                paste0("fit.models_1_", method), major.inc=TRUE)
    if (method %in% c("rpart", "rf")) {
        # rpart:    fubar's the tree
        # rf:       skip the scenario w/ .rnorm for speed
        indep_vars_vctr <- setdiff(indep_vars_vctr, c(".rnorm"))
        model_id <- paste0(model_id_pfx, ".no.rnorm")
    } else model_id <- model_id_pfx
    
    ret_lst <- myfit_mdl(model_id=model_id, model_method=method,
                            indep_vars_vctr=indep_vars_vctr,
                            model_type=glb_model_type,
                            rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                            fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df)
    
    # If All.X.glm is less accurate than Low.Cor.X.glm
    #   check NA coefficients & filter appropriate terms in indep_vars_vctr
#     if (method == "glm") {
#         orig_glm <- glb_models_lst[[paste0(model_id, ".", model_method)]]$finalModel
#         orig_glm <- glb_models_lst[["All.X.glm"]]$finalModel; print(summary(orig_glm))
#           vif_orig_glm <- vif(orig_glm); print(vif_orig_glm)
#           print(vif_orig_glm[!is.na(vif_orig_glm) & (vif_orig_glm == Inf)])
#           print(which.max(vif_orig_glm))
#           print(sort(vif_orig_glm[vif_orig_glm >= 1.0e+03], decreasing=TRUE))
#           glb_fitobs_df[c(1143, 3637, 3953, 4105), c("UniqueID", "Popular", "H.P.quandary", "Headline")]
#           glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.nchrs.log", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in%    grep("[HSA]\\.nchrs.log", glb_feats_df$id, value=TRUE), ]
#           glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.npnct14.log", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in%    grep("[HSA]\\.npnct14.log", glb_feats_df$id, value=TRUE), ]
#           glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.T.scen", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in%         grep("[HSA]\\.T.scen", glb_feats_df$id, value=TRUE), ]
#           glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.P.first", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in%         grep("[HSA]\\.P.first", glb_feats_df$id, value=TRUE), ]
#           all.equal(glb_allobs_df$S.nuppr.log, glb_allobs_df$A.nuppr.log)
#           all.equal(glb_allobs_df$S.npnct19.log, glb_allobs_df$A.npnct19.log)
#           all.equal(glb_allobs_df$S.P.year.colon, glb_allobs_df$A.P.year.colon)
#           all.equal(glb_allobs_df$S.T.share, glb_allobs_df$A.T.share)
#           all.equal(glb_allobs_df$H.T.clip, glb_allobs_df$H.P.daily.clip.report)
#           cor(glb_allobs_df$S.T.herald, glb_allobs_df$S.T.tribun)
#           dsp_obs(Abstract.contains="[Dd]iar", cols=("Abstract"), all=TRUE)
#           dsp_obs(Abstract.contains="[Ss]hare", cols=("Abstract"), all=TRUE)
#           subset(glb_feats_df, cor.y.abs <= glb_feats_df[glb_feats_df$id == ".rnorm", "cor.y.abs"])
#         corxx_mtrx <- cor(data.matrix(glb_allobs_df[, setdiff(names(glb_allobs_df), myfind_chr_cols_df(glb_allobs_df))]), use="pairwise.complete.obs"); abs_corxx_mtrx <- abs(corxx_mtrx); diag(abs_corxx_mtrx) <- 0
#           which.max(abs_corxx_mtrx["S.T.tribun", ])
#           abs_corxx_mtrx["A.npnct08.log", "S.npnct08.log"]
#         step_glm <- step(orig_glm)
#     }
    # Since caret does not optimize rpart well
#     if (method == "rpart")
#         ret_lst <- myfit_mdl(model_id=paste0(model_id_pfx, ".cp.0"), model_method=method,
#                                 indep_vars_vctr=indep_vars_vctr,
#                                 model_type=glb_model_type,
#                                 rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
#                                 fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,        
#             n_cv_folds=0, tune_models_df=data.frame(parameter="cp", min=0.0, max=0.0, by=0.1))
}
##              label step_major step_minor    bgn    end elapsed
## 1 fit.models_1_bgn          1          0 43.434 43.449   0.015
## 2 fit.models_1_glm          2          0 43.450     NA      NA
## [1] "fitting model: All.X.glm"
## [1] "    indep_vars: multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr"
## Aggregating results
## Fitting final model on full training set

## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.7256  -0.4288  -0.2719  -0.1681   2.8478  
## 
## Coefficients:
##                     Estimate Std. Error z value Pr(>|z|)    
## (Intercept)       -4.2474963  1.2952911  -3.279  0.00104 ** 
## multiple.offenses  1.6254434  0.3886164   4.183 2.88e-05 ***
## race               0.8823506  0.3953679   2.232  0.02563 *  
## age               -0.0003604  0.0160915  -0.022  0.98213    
## male               0.3878796  0.4385200   0.885  0.37642    
## .rnorm             0.0474484  0.1748880   0.271  0.78615    
## crime.fctr2        0.6720975  0.5030137   1.336  0.18150    
## crime.fctr3       -0.2805264  0.4328933  -0.648  0.51697    
## crime.fctr4       -0.0036558  0.5717918  -0.006  0.99490    
## time.served       -0.1219743  0.1205154  -1.012  0.31149    
## max.sentence       0.0801944  0.0554146   1.447  0.14785    
## state.fctr2        0.4585050  0.4855775   0.944  0.34504    
## state.fctr3        0.8535218  0.5607749   1.522  0.12800    
## state.fctr4       -3.3945448  0.6115599  -5.551 2.85e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 251.41  on 459  degrees of freedom
## AIC: 279.41
## 
## Number of Fisher Scoring iterations: 6
## 
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.4081633
## 3        0.2 0.4822695
## 4        0.3 0.4705882
## 5        0.4 0.4565217
## 6        0.5 0.4102564
## 7        0.6 0.2941176
## 8        0.7 0.2187500
## 9        0.8 0.1034483
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.2000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.All.X.glm.N
## 1             N                               366
## 2             Y                                21
##   violator.fctr.predict.All.X.glm.Y
## 1                                52
## 2                                34
##          Prediction
## Reference   N   Y
##         N 366  52
##         Y  21  34
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   0.8456659619   0.3966942149   0.8099028745   0.8770336126   0.8837209302 
## AccuracyPValue  McnemarPValue 
##   0.9947311468   0.0004460309 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold    f.score
## 1        0.0 0.20444444
## 2        0.1 0.43010753
## 3        0.2 0.52307692
## 4        0.3 0.50909091
## 5        0.4 0.52000000
## 6        0.5 0.54166667
## 7        0.6 0.25806452
## 8        0.7 0.20689655
## 9        0.8 0.22222222
## 10       0.9 0.08333333
## 11       1.0 0.00000000
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.All.X.glm.N
## 1             N                               167
## 2             Y                                10
##   violator.fctr.predict.All.X.glm.Y
## 1                                12
## 2                                13
##          Prediction
## Reference   N   Y
##         N 167  12
##         Y  10  13
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##      0.8910891      0.4799906      0.8397588      0.9304755      0.8861386 
## AccuracyPValue  McnemarPValue 
##      0.4672071      0.8311704 
##    model_id model_method
## 1 All.X.glm          glm
##                                                                                           feats
## 1 multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               1                      1.126                 0.012
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1    0.845759                    0.2       0.4822695         0.879505
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8099029             0.8770336     0.2015256   0.8938547
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.5       0.5416667        0.8910891
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1             0.8397588             0.9304755     0.4799906    279.4111
##   max.AccuracySD.fit max.KappaSD.fit
## 1        0.005969975      0.07399248
##                   label step_major step_minor    bgn   end elapsed
## 2      fit.models_1_glm          2          0 43.450 47.58    4.13
## 3 fit.models_1_bayesglm          3          0 47.581    NA      NA
## [1] "fitting model: All.X.bayesglm"
## [1] "    indep_vars: multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr"
## Loading required package: arm
## Loading required package: MASS
## 
## Attaching package: 'MASS'
## 
## The following object is masked from 'package:dplyr':
## 
##     select
## 
## Loading required package: Matrix
## Loading required package: lme4
## 
## arm (Version 1.8-5, built: 2015-05-13)
## 
## Working directory is /Users/bbalaji-2012/Documents/Work/Courses/MIT/Analytics_Edge_15_071x/Assignments/HW3-Parole-USNCRP2004

## Aggregating results
## Fitting final model on full training set
## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.6789  -0.4357  -0.2806  -0.1776   2.8086  
## 
## Coefficients:
##                     Estimate Std. Error z value Pr(>|z|)    
## (Intercept)       -4.0093654  1.2444856  -3.222  0.00127 ** 
## multiple.offenses  1.5336810  0.3758544   4.081 4.49e-05 ***
## race               0.8201912  0.3783187   2.168  0.03016 *  
## age               -0.0001381  0.0156116  -0.009  0.99294    
## male               0.3421396  0.4191064   0.816  0.41430    
## .rnorm             0.0412254  0.1697242   0.243  0.80809    
## crime.fctr2        0.6046822  0.4781696   1.265  0.20602    
## crime.fctr3       -0.2598157  0.4135320  -0.628  0.52982    
## crime.fctr4       -0.0357646  0.5385920  -0.066  0.94706    
## time.served       -0.1198810  0.1173092  -1.022  0.30682    
## max.sentence       0.0735864  0.0534918   1.376  0.16893    
## state.fctr2        0.4054643  0.4610667   0.879  0.37918    
## state.fctr3        0.8448562  0.5245248   1.611  0.10724    
## state.fctr4       -3.2265378  0.5744837  -5.616 1.95e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 251.56  on 459  degrees of freedom
## AIC: 279.56
## 
## Number of Fisher Scoring iterations: 9
## 
## [1] "    calling mypredict_mdl for fit:"

##    threshold    f.score
## 1        0.0 0.20833333
## 2        0.1 0.40404040
## 3        0.2 0.48920863
## 4        0.3 0.45544554
## 5        0.4 0.43181818
## 6        0.5 0.36842105
## 7        0.6 0.26865672
## 8        0.7 0.19354839
## 9        0.8 0.03571429
## 10       0.9 0.00000000
## 11       1.0 0.00000000

## [1] "Classifier Probability Threshold: 0.2000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.All.X.bayesglm.N
## 1             N                                    368
## 2             Y                                     21
##   violator.fctr.predict.All.X.bayesglm.Y
## 1                                     50
## 2                                     34
##          Prediction
## Reference   N   Y
##         N 368  50
##         Y  21  34
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   0.8498942918   0.4056842515   0.8144698116   0.8808675533   0.8837209302 
## AccuracyPValue  McnemarPValue 
##   0.9890715453   0.0008905854 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold   f.score
## 1        0.0 0.2044444
## 2        0.1 0.4421053
## 3        0.2 0.5151515
## 4        0.3 0.5090909
## 5        0.4 0.5306122
## 6        0.5 0.5217391
## 7        0.6 0.2580645
## 8        0.7 0.2068966
## 9        0.8 0.1538462
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.4000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.All.X.bayesglm.N
## 1             N                                    166
## 2             Y                                     10
##   violator.fctr.predict.All.X.bayesglm.Y
## 1                                     13
## 2                                     13
##          Prediction
## Reference   N   Y
##         N 166  13
##         Y  10  13
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##      0.8861386      0.4660997      0.8340624      0.9264369      0.8861386 
## AccuracyPValue  McnemarPValue 
##      0.5552509      0.6766573 
##         model_id model_method
## 1 All.X.bayesglm     bayesglm
##                                                                                           feats
## 1 multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               1                      1.813                 0.031
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1   0.8452371                    0.2       0.4892086        0.8816281
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8144698             0.8808676     0.2071379   0.8945834
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.4       0.5306122        0.8861386
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1             0.8340624             0.9264369     0.4660997    279.5551
##   max.AccuracySD.fit max.KappaSD.fit
## 1        0.009294912      0.06810481
##                   label step_major step_minor    bgn   end elapsed
## 3 fit.models_1_bayesglm          3          0 47.581 51.86   4.279
## 4    fit.models_1_rpart          4          0 51.861    NA      NA
## [1] "fitting model: All.X.no.rnorm.rpart"
## [1] "    indep_vars: multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr"
## Aggregating results
## Selecting tuning parameters
## Fitting cp = 0.0485 on full training set
## Warning in myfit_mdl(model_id = model_id, model_method = method,
## indep_vars_vctr = indep_vars_vctr, : model's bestTune found at an extreme
## of tuneGrid for parameter: cp

## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7, 
##     cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, 
##     surrogatestyle = 0, maxdepth = 30, xval = 0))
##   n= 473 
## 
##           CP nsplit rel error
## 1 0.04848485      0         1
## 
## Node number 1: 473 observations
##   predicted class=N  expected loss=0.1162791  P(node) =1
##     class counts:   418    55
##    probabilities: 0.884 0.116 
## 
## n= 473 
## 
## node), split, n, loss, yval, (yprob)
##       * denotes terminal node
## 
## 1) root 473 55 N (0.8837209 0.1162791) *
## [1] "    calling mypredict_mdl for fit:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.All.X.no.rnorm.rpart.N
## 1             N                                          418
## 2             Y                                           55
##          Prediction
## Reference   N   Y
##         N 418   0
##         Y  55   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.837209e-01   0.000000e+00   8.513472e-01   9.111909e-01   8.837209e-01 
## AccuracyPValue  McnemarPValue 
##   5.358475e-01   3.304751e-13 
## [1] "    calling mypredict_mdl for OOB:"
## [1] "Classifier Probability Threshold: 0.5000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.All.X.no.rnorm.rpart.N
## 1             N                                          179
## 2             Y                                           23
##          Prediction
## Reference   N   Y
##         N 179   0
##         Y  23   0
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   8.861386e-01   0.000000e+00   8.340624e-01   9.264369e-01   8.861386e-01 
## AccuracyPValue  McnemarPValue 
##   5.552509e-01   4.489784e-06 
##               model_id model_method
## 1 All.X.no.rnorm.rpart        rpart
##                                                                                   feats
## 1 multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               3                      0.952                 0.013
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1         0.5                    0.5               0         0.879505
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8513472             0.9111909     0.1393519         0.5
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.5               0        0.8861386
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1             0.8340624             0.9264369             0
##   max.AccuracySD.fit max.KappaSD.fit
## 1         0.01075899       0.1309123
##                label step_major step_minor    bgn    end elapsed
## 4 fit.models_1_rpart          4          0 51.861 54.545   2.684
## 5    fit.models_1_rf          5          0 54.545     NA      NA
## [1] "fitting model: All.X.no.rnorm.rf"
## [1] "    indep_vars: multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr"
## Loading required package: randomForest
## randomForest 4.6-10
## Type rfNews() to see new features/changes/bug fixes.
## 
## Attaching package: 'randomForest'
## 
## The following object is masked from 'package:dplyr':
## 
##     combine

## Aggregating results
## Selecting tuning parameters
## Fitting mtry = 7 on full training set

##                 Length Class      Mode     
## call               4   -none-     call     
## type               1   -none-     character
## predicted        473   factor     numeric  
## err.rate        1500   -none-     numeric  
## confusion          6   -none-     numeric  
## votes            946   matrix     numeric  
## oob.times        473   -none-     numeric  
## classes            2   -none-     character
## importance        12   -none-     numeric  
## importanceSD       0   -none-     NULL     
## localImportance    0   -none-     NULL     
## proximity          0   -none-     NULL     
## ntree              1   -none-     numeric  
## mtry               1   -none-     numeric  
## forest            14   -none-     list     
## y                473   factor     numeric  
## test               0   -none-     NULL     
## inbag              0   -none-     NULL     
## xNames            12   -none-     character
## problemType        1   -none-     character
## tuneValue          1   data.frame list     
## obsLevels          2   -none-     character
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.6707317
## 3        0.2 0.9090909
## 4        0.3 0.9909910
## 5        0.4 1.0000000
## 6        0.5 1.0000000
## 7        0.6 1.0000000
## 8        0.7 0.8172043
## 9        0.8 0.4931507
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.6000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.All.X.no.rnorm.rf.N
## 1             N                                       418
## 2             Y                                        NA
##   violator.fctr.predict.All.X.no.rnorm.rf.Y
## 1                                        NA
## 2                                        55
##          Prediction
## Reference   N   Y
##         N 418   0
##         Y   0  55
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   1.000000e+00   1.000000e+00   9.922314e-01   1.000000e+00   8.837209e-01 
## AccuracyPValue  McnemarPValue 
##   4.046334e-26            NaN 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold   f.score
## 1        0.0 0.2044444
## 2        0.1 0.4400000
## 3        0.2 0.4750000
## 4        0.3 0.5245902
## 5        0.4 0.5000000
## 6        0.5 0.4255319
## 7        0.6 0.3888889
## 8        0.7 0.2068966
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.3000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.All.X.no.rnorm.rf.N
## 1             N                                       157
## 2             Y                                         7
##   violator.fctr.predict.All.X.no.rnorm.rf.Y
## 1                                        22
## 2                                        16
##          Prediction
## Reference   N   Y
##         N 157  22
##         Y   7  16
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##    0.856435644    0.445999622    0.800367596    0.901697429    0.886138614 
## AccuracyPValue  McnemarPValue 
##    0.921326669    0.009329585 
##            model_id model_method
## 1 All.X.no.rnorm.rf           rf
##                                                                                   feats
## 1 multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               3                      3.377                 0.605
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1           1                    0.6               1        0.8942863
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.9922314                     1     0.2424736   0.8796454
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.3       0.5245902        0.8564356
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB
## 1             0.8003676             0.9016974     0.4459996
##   max.AccuracySD.fit max.KappaSD.fit
## 1        0.003867161      0.09115572
# User specified
#   Ensure at least 2 vars in each regression; else varImp crashes
# sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df; sav_featsimp_df <- glb_featsimp_df
# glb_models_lst <- sav_models_lst; glb_models_df <- sav_models_df; glm_featsimp_df <- sav_featsimp_df

    # easier to exclude features
# require(gdata) # needed for trim
# model_id <- "";
# indep_vars_vctr <- head(subset(glb_models_df, grepl("All\\.X\\.", model_id), select=feats)
#                         , 1)[, "feats"]
# indep_vars_vctr <- trim(unlist(strsplit(indep_vars_vctr, "[,]")))
# indep_vars_vctr <- setdiff(indep_vars_vctr, ".rnorm")

    # easier to include features
model_id <- "Csm.1"; indep_vars_vctr <- c("multiple.offenses", "race", "state.fctr")
for (method in c("glm")) {
    ret_lst <- myfit_mdl(model_id=model_id, model_method=method,
                                indep_vars_vctr=indep_vars_vctr,
                                model_type=glb_model_type,
                                rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
                                fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
                    n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df)
    csm_mdl_id <- paste0(model_id, ".", method)
    csm_featsimp_df <- myget_feats_importance(glb_models_lst[[paste0(model_id, ".", method)]]);         print(head(csm_featsimp_df))
}
## [1] "fitting model: Csm.1.glm"
## [1] "    indep_vars: multiple.offenses, race, state.fctr"
## Aggregating results
## Fitting final model on full training set

## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.4422  -0.4430  -0.2922  -0.1917   2.8306  
## 
## Coefficients:
##                   Estimate Std. Error z value Pr(>|z|)    
## (Intercept)        -3.3018     0.5735  -5.757 8.55e-09 ***
## multiple.offenses   1.5589     0.3759   4.147 3.37e-05 ***
## race                0.8553     0.3789   2.257    0.024 *  
## state.fctr2         0.1742     0.4438   0.393    0.695    
## state.fctr3         0.6362     0.4716   1.349    0.177    
## state.fctr4        -3.1003     0.5798  -5.347 8.96e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 258.53  on 467  degrees of freedom
## AIC: 270.53
## 
## Number of Fisher Scoring iterations: 6
## 
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.4378698
## 3        0.2 0.4776119
## 4        0.3 0.4210526
## 5        0.4 0.4318182
## 6        0.5 0.3947368
## 7        0.6 0.3513514
## 8        0.7 0.0000000
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.2000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Csm.1.glm.N
## 1             N                               371
## 2             Y                                23
##   violator.fctr.predict.Csm.1.glm.Y
## 1                                47
## 2                                32
##          Prediction
## Reference   N   Y
##         N 371  47
##         Y  23  32
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##    0.852008457    0.394609815    0.816756519    0.882781231    0.883720930 
## AccuracyPValue  McnemarPValue 
##    0.984599818    0.005977268 
## [1] "    calling mypredict_mdl for OOB:"

##    threshold   f.score
## 1        0.0 0.2044444
## 2        0.1 0.5384615
## 3        0.2 0.5714286
## 4        0.3 0.5185185
## 5        0.4 0.5490196
## 6        0.5 0.5000000
## 7        0.6 0.5116279
## 8        0.7 0.0000000
## 9        0.8 0.0000000
## 10       0.9 0.0000000
## 11       1.0 0.0000000

## [1] "Classifier Probability Threshold: 0.2000 to maximize f.score.OOB"
##   violator.fctr violator.fctr.predict.Csm.1.glm.N
## 1             N                               157
## 2             Y                                 5
##   violator.fctr.predict.Csm.1.glm.Y
## 1                                22
## 2                                18
##          Prediction
## Reference   N   Y
##         N 157  22
##         Y   5  18
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##    0.866336634    0.498989528    0.811514363    0.910032607    0.886138614 
## AccuracyPValue  McnemarPValue 
##    0.840894507    0.002075563 
##    model_id model_method                               feats
## 1 Csm.1.glm          glm multiple.offenses, race, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               1                       0.88                 0.009
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1   0.8287516                    0.2       0.4776119        0.8922304
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## 1             0.8167565             0.8827812      0.323349   0.9023561
##   opt.prob.threshold.OOB max.f.score.OOB max.Accuracy.OOB
## 1                    0.2       0.5714286        0.8663366
##   max.AccuracyLower.OOB max.AccuracyUpper.OOB max.Kappa.OOB min.aic.fit
## 1             0.8115144             0.9100326     0.4989895    270.5307
##   max.AccuracySD.fit max.KappaSD.fit
## 1          0.0225294        0.112294
##                   importance
## state.fctr4        100.00000
## multiple.offenses   75.78700
## race                37.63986
## state.fctr3         19.30695
## state.fctr2          0.00000
# Ntv.1.lm <- lm(reformulate(indep_vars_vctr, glb_rsp_var), glb_trnobs_df); print(summary(Ntv.1.lm))

#print(dsp_models_df <- orderBy(model_sel_frmla, glb_models_df)[, dsp_models_cols])
#csm_featsimp_df[grepl("H.npnct19.log", row.names(csm_featsimp_df)), , FALSE]
#csm_OOBobs_df <- glb_get_predictions(glb_OOBobs_df, mdl_id=csm_mdl_id, rsp_var_out=glb_rsp_var_out, prob_threshold_def=glb_models_df[glb_models_df$model_id == csm_mdl_id, "opt.prob.threshold.OOB"])
#print(sprintf("%s OOB confusion matrix & accuracy: ", csm_mdl_id)); print(t(confusionMatrix(csm_OOBobs_df[, paste0(glb_rsp_var_out, csm_mdl_id)], csm_OOBobs_df[, glb_rsp_var])$table))

#glb_models_df[, "max.Accuracy.OOB", FALSE]
#varImp(glb_models_lst[["Low.cor.X.glm"]])
#orderBy(~ -Overall, varImp(glb_models_lst[["All.X.2.glm"]])$importance)
#orderBy(~ -Overall, varImp(glb_models_lst[["All.X.3.glm"]])$importance)
#glb_feats_df[grepl("npnct28", glb_feats_df$id), ]
#print(sprintf("%s OOB confusion matrix & accuracy: ", glb_sel_mdl_id)); print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)], glb_OOBobs_df[, glb_rsp_var])$table))

    # User specified bivariate models
#     indep_vars_vctr_lst <- list()
#     for (feat in setdiff(names(glb_fitobs_df), 
#                          union(glb_rsp_var, glb_exclude_vars_as_features)))
#         indep_vars_vctr_lst[["feat"]] <- feat

    # User specified combinatorial models
#     indep_vars_vctr_lst <- list()
#     combn_mtrx <- combn(c("<feat1_name>", "<feat2_name>", "<featn_name>"), 
#                           <num_feats_to_choose>)
#     for (combn_ix in 1:ncol(combn_mtrx))
#         #print(combn_mtrx[, combn_ix])
#         indep_vars_vctr_lst[[combn_ix]] <- combn_mtrx[, combn_ix]
    
    # template for myfit_mdl
    #   rf is hard-coded in caret to recognize only Accuracy / Kappa evaluation metrics
    #       only for OOB in trainControl ?
    
#     ret_lst <- myfit_mdl_fn(model_id=paste0(model_id_pfx, ""), model_method=method,
#                             indep_vars_vctr=indep_vars_vctr,
#                             rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
#                             fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
#                             n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df,
#                             model_loss_mtrx=glb_model_metric_terms,
#                             model_summaryFunction=glb_model_metric_smmry,
#                             model_metric=glb_model_metric,
#                             model_metric_maximize=glb_model_metric_maximize)

# Simplify a model
# fit_df <- glb_fitobs_df; glb_mdl <- step(<complex>_mdl)

# Non-caret models
#     rpart_area_mdl <- rpart(reformulate("Area", response=glb_rsp_var), 
#                                data=glb_fitobs_df, #method="class", 
#                                control=rpart.control(cp=0.12),
#                            parms=list(loss=glb_model_metric_terms))
#     print("rpart_sel_wlm_mdl"); prp(rpart_sel_wlm_mdl)
# 

print(glb_models_df)
##                                            model_id     model_method
## MFO.myMFO_classfr                 MFO.myMFO_classfr    myMFO_classfr
## Random.myrandom_classfr     Random.myrandom_classfr myrandom_classfr
## Max.cor.Y.cv.0.rpart           Max.cor.Y.cv.0.rpart            rpart
## Max.cor.Y.cv.0.cp.0.rpart Max.cor.Y.cv.0.cp.0.rpart            rpart
## Max.cor.Y.rpart                     Max.cor.Y.rpart            rpart
## Max.cor.Y.glm                         Max.cor.Y.glm              glm
## Low.cor.X.glm                         Low.cor.X.glm              glm
## All.X.glm                                 All.X.glm              glm
## All.X.bayesglm                       All.X.bayesglm         bayesglm
## All.X.no.rnorm.rpart           All.X.no.rnorm.rpart            rpart
## All.X.no.rnorm.rf                 All.X.no.rnorm.rf               rf
## Csm.1.glm                                 Csm.1.glm              glm
##                                                                                                                   feats
## MFO.myMFO_classfr                                                                                                .rnorm
## Random.myrandom_classfr                                                                                          .rnorm
## Max.cor.Y.cv.0.rpart                                                                           state.fctr, max.sentence
## Max.cor.Y.cv.0.cp.0.rpart                                                                      state.fctr, max.sentence
## Max.cor.Y.rpart                                                                                state.fctr, max.sentence
## Max.cor.Y.glm                                                                                  state.fctr, max.sentence
## Low.cor.X.glm             multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
## All.X.glm                 multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
## All.X.bayesglm            multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
## All.X.no.rnorm.rpart              multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr
## All.X.no.rnorm.rf                 multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr
## Csm.1.glm                                                                           multiple.offenses, race, state.fctr
##                           max.nTuningRuns min.elapsedtime.everything
## MFO.myMFO_classfr                       0                      0.407
## Random.myrandom_classfr                 0                      0.231
## Max.cor.Y.cv.0.rpart                    0                      0.620
## Max.cor.Y.cv.0.cp.0.rpart               0                      0.448
## Max.cor.Y.rpart                         3                      0.997
## Max.cor.Y.glm                           1                      0.884
## Low.cor.X.glm                           1                      1.140
## All.X.glm                               1                      1.126
## All.X.bayesglm                          1                      1.813
## All.X.no.rnorm.rpart                    3                      0.952
## All.X.no.rnorm.rf                       3                      3.377
## Csm.1.glm                               1                      0.880
##                           min.elapsedtime.final max.auc.fit
## MFO.myMFO_classfr                         0.003   0.5000000
## Random.myrandom_classfr                   0.001   0.5224880
## Max.cor.Y.cv.0.rpart                      0.010   0.5000000
## Max.cor.Y.cv.0.cp.0.rpart                 0.007   0.6612223
## Max.cor.Y.rpart                           0.010   0.5000000
## Max.cor.Y.glm                             0.011   0.8018486
## Low.cor.X.glm                             0.012   0.8457590
## All.X.glm                                 0.012   0.8457590
## All.X.bayesglm                            0.031   0.8452371
## All.X.no.rnorm.rpart                      0.013   0.5000000
## All.X.no.rnorm.rf                         0.605   1.0000000
## Csm.1.glm                                 0.009   0.8287516
##                           opt.prob.threshold.fit max.f.score.fit
## MFO.myMFO_classfr                            0.5       0.0000000
## Random.myrandom_classfr                      0.1       0.2083333
## Max.cor.Y.cv.0.rpart                         0.5       0.0000000
## Max.cor.Y.cv.0.cp.0.rpart                    0.3       0.4077670
## Max.cor.Y.rpart                              0.5       0.0000000
## Max.cor.Y.glm                                0.3       0.4077670
## Low.cor.X.glm                                0.2       0.4822695
## All.X.glm                                    0.2       0.4822695
## All.X.bayesglm                               0.2       0.4892086
## All.X.no.rnorm.rpart                         0.5       0.0000000
## All.X.no.rnorm.rf                            0.6       1.0000000
## Csm.1.glm                                    0.2       0.4776119
##                           max.Accuracy.fit max.AccuracyLower.fit
## MFO.myMFO_classfr                0.8837209            0.85134724
## Random.myrandom_classfr          0.1162791            0.08880912
## Max.cor.Y.cv.0.rpart             0.8837209            0.85134724
## Max.cor.Y.cv.0.cp.0.rpart        0.8710359            0.83744135
## Max.cor.Y.rpart                  0.8773953            0.85134724
## Max.cor.Y.glm                    0.8795050            0.83744135
## Low.cor.X.glm                    0.8795050            0.80990287
## All.X.glm                        0.8795050            0.80990287
## All.X.bayesglm                   0.8816281            0.81446981
## All.X.no.rnorm.rpart             0.8795050            0.85134724
## All.X.no.rnorm.rf                0.8942863            0.99223143
## Csm.1.glm                        0.8922304            0.81675652
##                           max.AccuracyUpper.fit max.Kappa.fit max.auc.OOB
## MFO.myMFO_classfr                     0.9111909     0.0000000   0.5000000
## Random.myrandom_classfr               0.1486528     0.0000000   0.4602866
## Max.cor.Y.cv.0.rpart                  0.9111909     0.0000000   0.5000000
## Max.cor.Y.cv.0.cp.0.rpart             0.8998980     0.3357812   0.7951178
## Max.cor.Y.rpart                       0.9111909     0.1504134   0.5000000
## Max.cor.Y.glm                         0.8998980     0.1380265   0.8581491
## Low.cor.X.glm                         0.8770336     0.2015256   0.8938547
## All.X.glm                             0.8770336     0.2015256   0.8938547
## All.X.bayesglm                        0.8808676     0.2071379   0.8945834
## All.X.no.rnorm.rpart                  0.9111909     0.1393519   0.5000000
## All.X.no.rnorm.rf                     1.0000000     0.2424736   0.8796454
## Csm.1.glm                             0.8827812     0.3233490   0.9023561
##                           opt.prob.threshold.OOB max.f.score.OOB
## MFO.myMFO_classfr                            0.5       0.0000000
## Random.myrandom_classfr                      0.1       0.2044444
## Max.cor.Y.cv.0.rpart                         0.5       0.0000000
## Max.cor.Y.cv.0.cp.0.rpart                    0.3       0.5614035
## Max.cor.Y.rpart                              0.5       0.0000000
## Max.cor.Y.glm                                0.3       0.5614035
## Low.cor.X.glm                                0.5       0.5416667
## All.X.glm                                    0.5       0.5416667
## All.X.bayesglm                               0.4       0.5306122
## All.X.no.rnorm.rpart                         0.5       0.0000000
## All.X.no.rnorm.rf                            0.3       0.5245902
## Csm.1.glm                                    0.2       0.5714286
##                           max.Accuracy.OOB max.AccuracyLower.OOB
## MFO.myMFO_classfr                0.8861386            0.83406236
## Random.myrandom_classfr          0.1138614            0.07356311
## Max.cor.Y.cv.0.rpart             0.8861386            0.83406236
## Max.cor.Y.cv.0.cp.0.rpart        0.8762376            0.82274322
## Max.cor.Y.rpart                  0.8861386            0.83406236
## Max.cor.Y.glm                    0.8762376            0.82274322
## Low.cor.X.glm                    0.8910891            0.83975881
## All.X.glm                        0.8910891            0.83975881
## All.X.bayesglm                   0.8861386            0.83406236
## All.X.no.rnorm.rpart             0.8861386            0.83406236
## All.X.no.rnorm.rf                0.8564356            0.80036760
## Csm.1.glm                        0.8663366            0.81151436
##                           max.AccuracyUpper.OOB max.Kappa.OOB
## MFO.myMFO_classfr                     0.9264369     0.0000000
## Random.myrandom_classfr               0.1659376     0.0000000
## Max.cor.Y.cv.0.rpart                  0.9264369     0.0000000
## Max.cor.Y.cv.0.cp.0.rpart             0.9182821     0.4924623
## Max.cor.Y.rpart                       0.9264369     0.0000000
## Max.cor.Y.glm                         0.9182821     0.4924623
## Low.cor.X.glm                         0.9304755     0.4799906
## All.X.glm                             0.9304755     0.4799906
## All.X.bayesglm                        0.9264369     0.4660997
## All.X.no.rnorm.rpart                  0.9264369     0.0000000
## All.X.no.rnorm.rf                     0.9016974     0.4459996
## Csm.1.glm                             0.9100326     0.4989895
##                           max.AccuracySD.fit max.KappaSD.fit min.aic.fit
## MFO.myMFO_classfr                         NA              NA          NA
## Random.myrandom_classfr                   NA              NA          NA
## Max.cor.Y.cv.0.rpart                      NA              NA          NA
## Max.cor.Y.cv.0.cp.0.rpart                 NA              NA          NA
## Max.cor.Y.rpart                  0.014411559      0.13364427          NA
## Max.cor.Y.glm                    0.005969975      0.12100848    288.5369
## Low.cor.X.glm                    0.005969975      0.07399248    279.4111
## All.X.glm                        0.005969975      0.07399248    279.4111
## All.X.bayesglm                   0.009294912      0.06810481    279.5551
## All.X.no.rnorm.rpart             0.010758994      0.13091227          NA
## All.X.no.rnorm.rf                0.003867161      0.09115572          NA
## Csm.1.glm                        0.022529401      0.11229405    270.5307
rm(ret_lst)
fit.models_1_chunk_df <- myadd_chunk(fit.models_1_chunk_df, "fit.models_1_end", 
                                     major.inc=TRUE)
##              label step_major step_minor    bgn    end elapsed
## 5  fit.models_1_rf          5          0 54.545 64.773  10.228
## 6 fit.models_1_end          6          0 64.773     NA      NA
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)
##         label step_major step_minor    bgn   end elapsed
## 11 fit.models          7          1 41.151 64.78  23.629
## 12 fit.models          7          2 64.781    NA      NA
if (!is.null(glb_model_metric_smmry)) {
    stats_df <- glb_models_df[, "model_id", FALSE]

    stats_mdl_df <- data.frame()
    for (model_id in stats_df$model_id) {
        stats_mdl_df <- rbind(stats_mdl_df, 
            mypredict_mdl(glb_models_lst[[model_id]], glb_fitobs_df, glb_rsp_var, 
                          glb_rsp_var_out, model_id, "fit",
                                glb_model_metric_smmry, glb_model_metric, 
                                glb_model_metric_maximize, ret_type="stats"))
    }
    stats_df <- merge(stats_df, stats_mdl_df, all.x=TRUE)
    
    stats_mdl_df <- data.frame()
    for (model_id in stats_df$model_id) {
        stats_mdl_df <- rbind(stats_mdl_df, 
            mypredict_mdl(glb_models_lst[[model_id]], glb_OOBobs_df, glb_rsp_var, 
                          glb_rsp_var_out, model_id, "OOB",
                                glb_model_metric_smmry, glb_model_metric, 
                                glb_model_metric_maximize, ret_type="stats"))
    }
    stats_df <- merge(stats_df, stats_mdl_df, all.x=TRUE)
    
    print("Merging following data into glb_models_df:")
    print(stats_mrg_df <- stats_df[, c(1, grep(glb_model_metric, names(stats_df)))])
    print(tmp_models_df <- orderBy(~model_id, glb_models_df[, c("model_id",
                                    grep(glb_model_metric, names(stats_df), value=TRUE))]))

    tmp2_models_df <- glb_models_df[, c("model_id", setdiff(names(glb_models_df),
                                    grep(glb_model_metric, names(stats_df), value=TRUE)))]
    tmp3_models_df <- merge(tmp2_models_df, stats_mrg_df, all.x=TRUE, sort=FALSE)
    print(tmp3_models_df)
    print(names(tmp3_models_df))
    print(glb_models_df <- subset(tmp3_models_df, select=-model_id.1))
}

plt_models_df <- glb_models_df[, -grep("SD|Upper|Lower", names(glb_models_df))]
for (var in grep("^min.", names(plt_models_df), value=TRUE)) {
    plt_models_df[, sub("min.", "inv.", var)] <- 
        #ifelse(all(is.na(tmp <- plt_models_df[, var])), NA, 1.0 / tmp)
        1.0 / plt_models_df[, var]
    plt_models_df <- plt_models_df[ , -grep(var, names(plt_models_df))]
}
print(plt_models_df)
##                                            model_id     model_method
## MFO.myMFO_classfr                 MFO.myMFO_classfr    myMFO_classfr
## Random.myrandom_classfr     Random.myrandom_classfr myrandom_classfr
## Max.cor.Y.cv.0.rpart           Max.cor.Y.cv.0.rpart            rpart
## Max.cor.Y.cv.0.cp.0.rpart Max.cor.Y.cv.0.cp.0.rpart            rpart
## Max.cor.Y.rpart                     Max.cor.Y.rpart            rpart
## Max.cor.Y.glm                         Max.cor.Y.glm              glm
## Low.cor.X.glm                         Low.cor.X.glm              glm
## All.X.glm                                 All.X.glm              glm
## All.X.bayesglm                       All.X.bayesglm         bayesglm
## All.X.no.rnorm.rpart           All.X.no.rnorm.rpart            rpart
## All.X.no.rnorm.rf                 All.X.no.rnorm.rf               rf
## Csm.1.glm                                 Csm.1.glm              glm
##                                                                                                                   feats
## MFO.myMFO_classfr                                                                                                .rnorm
## Random.myrandom_classfr                                                                                          .rnorm
## Max.cor.Y.cv.0.rpart                                                                           state.fctr, max.sentence
## Max.cor.Y.cv.0.cp.0.rpart                                                                      state.fctr, max.sentence
## Max.cor.Y.rpart                                                                                state.fctr, max.sentence
## Max.cor.Y.glm                                                                                  state.fctr, max.sentence
## Low.cor.X.glm             multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
## All.X.glm                 multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
## All.X.bayesglm            multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
## All.X.no.rnorm.rpart              multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr
## All.X.no.rnorm.rf                 multiple.offenses, race, age, male, crime.fctr, time.served, max.sentence, state.fctr
## Csm.1.glm                                                                           multiple.offenses, race, state.fctr
##                           max.nTuningRuns max.auc.fit
## MFO.myMFO_classfr                       0   0.5000000
## Random.myrandom_classfr                 0   0.5224880
## Max.cor.Y.cv.0.rpart                    0   0.5000000
## Max.cor.Y.cv.0.cp.0.rpart               0   0.6612223
## Max.cor.Y.rpart                         3   0.5000000
## Max.cor.Y.glm                           1   0.8018486
## Low.cor.X.glm                           1   0.8457590
## All.X.glm                               1   0.8457590
## All.X.bayesglm                          1   0.8452371
## All.X.no.rnorm.rpart                    3   0.5000000
## All.X.no.rnorm.rf                       3   1.0000000
## Csm.1.glm                               1   0.8287516
##                           opt.prob.threshold.fit max.f.score.fit
## MFO.myMFO_classfr                            0.5       0.0000000
## Random.myrandom_classfr                      0.1       0.2083333
## Max.cor.Y.cv.0.rpart                         0.5       0.0000000
## Max.cor.Y.cv.0.cp.0.rpart                    0.3       0.4077670
## Max.cor.Y.rpart                              0.5       0.0000000
## Max.cor.Y.glm                                0.3       0.4077670
## Low.cor.X.glm                                0.2       0.4822695
## All.X.glm                                    0.2       0.4822695
## All.X.bayesglm                               0.2       0.4892086
## All.X.no.rnorm.rpart                         0.5       0.0000000
## All.X.no.rnorm.rf                            0.6       1.0000000
## Csm.1.glm                                    0.2       0.4776119
##                           max.Accuracy.fit max.Kappa.fit max.auc.OOB
## MFO.myMFO_classfr                0.8837209     0.0000000   0.5000000
## Random.myrandom_classfr          0.1162791     0.0000000   0.4602866
## Max.cor.Y.cv.0.rpart             0.8837209     0.0000000   0.5000000
## Max.cor.Y.cv.0.cp.0.rpart        0.8710359     0.3357812   0.7951178
## Max.cor.Y.rpart                  0.8773953     0.1504134   0.5000000
## Max.cor.Y.glm                    0.8795050     0.1380265   0.8581491
## Low.cor.X.glm                    0.8795050     0.2015256   0.8938547
## All.X.glm                        0.8795050     0.2015256   0.8938547
## All.X.bayesglm                   0.8816281     0.2071379   0.8945834
## All.X.no.rnorm.rpart             0.8795050     0.1393519   0.5000000
## All.X.no.rnorm.rf                0.8942863     0.2424736   0.8796454
## Csm.1.glm                        0.8922304     0.3233490   0.9023561
##                           opt.prob.threshold.OOB max.f.score.OOB
## MFO.myMFO_classfr                            0.5       0.0000000
## Random.myrandom_classfr                      0.1       0.2044444
## Max.cor.Y.cv.0.rpart                         0.5       0.0000000
## Max.cor.Y.cv.0.cp.0.rpart                    0.3       0.5614035
## Max.cor.Y.rpart                              0.5       0.0000000
## Max.cor.Y.glm                                0.3       0.5614035
## Low.cor.X.glm                                0.5       0.5416667
## All.X.glm                                    0.5       0.5416667
## All.X.bayesglm                               0.4       0.5306122
## All.X.no.rnorm.rpart                         0.5       0.0000000
## All.X.no.rnorm.rf                            0.3       0.5245902
## Csm.1.glm                                    0.2       0.5714286
##                           max.Accuracy.OOB max.Kappa.OOB
## MFO.myMFO_classfr                0.8861386     0.0000000
## Random.myrandom_classfr          0.1138614     0.0000000
## Max.cor.Y.cv.0.rpart             0.8861386     0.0000000
## Max.cor.Y.cv.0.cp.0.rpart        0.8762376     0.4924623
## Max.cor.Y.rpart                  0.8861386     0.0000000
## Max.cor.Y.glm                    0.8762376     0.4924623
## Low.cor.X.glm                    0.8910891     0.4799906
## All.X.glm                        0.8910891     0.4799906
## All.X.bayesglm                   0.8861386     0.4660997
## All.X.no.rnorm.rpart             0.8861386     0.0000000
## All.X.no.rnorm.rf                0.8564356     0.4459996
## Csm.1.glm                        0.8663366     0.4989895
##                           inv.elapsedtime.everything inv.elapsedtime.final
## MFO.myMFO_classfr                          2.4570025            333.333333
## Random.myrandom_classfr                    4.3290043           1000.000000
## Max.cor.Y.cv.0.rpart                       1.6129032            100.000000
## Max.cor.Y.cv.0.cp.0.rpart                  2.2321429            142.857143
## Max.cor.Y.rpart                            1.0030090            100.000000
## Max.cor.Y.glm                              1.1312217             90.909091
## Low.cor.X.glm                              0.8771930             83.333333
## All.X.glm                                  0.8880995             83.333333
## All.X.bayesglm                             0.5515720             32.258065
## All.X.no.rnorm.rpart                       1.0504202             76.923077
## All.X.no.rnorm.rf                          0.2961208              1.652893
## Csm.1.glm                                  1.1363636            111.111111
##                           inv.aic.fit
## MFO.myMFO_classfr                  NA
## Random.myrandom_classfr            NA
## Max.cor.Y.cv.0.rpart               NA
## Max.cor.Y.cv.0.cp.0.rpart          NA
## Max.cor.Y.rpart                    NA
## Max.cor.Y.glm             0.003465761
## Low.cor.X.glm             0.003578956
## All.X.glm                 0.003578956
## All.X.bayesglm            0.003577112
## All.X.no.rnorm.rpart               NA
## All.X.no.rnorm.rf                  NA
## Csm.1.glm                 0.003696438
print(myplot_radar(radar_inp_df=plt_models_df))
## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors
## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.
## Warning: Removed 4 rows containing missing values (geom_path).
## Warning: Removed 87 rows containing missing values (geom_point).
## Warning: Removed 7 rows containing missing values (geom_text).
## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors
## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.

# print(myplot_radar(radar_inp_df=subset(plt_models_df, 
#         !(model_id %in% grep("random|MFO", plt_models_df$model_id, value=TRUE)))))

# Compute CI for <metric>SD
glb_models_df <- mutate(glb_models_df, 
                max.df = ifelse(max.nTuningRuns > 1, max.nTuningRuns - 1, NA),
                min.sd2ci.scaler = ifelse(is.na(max.df), NA, qt(0.975, max.df)))
for (var in grep("SD", names(glb_models_df), value=TRUE)) {
    # Does CI alredy exist ?
    var_components <- unlist(strsplit(var, "SD"))
    varActul <- paste0(var_components[1],          var_components[2])
    varUpper <- paste0(var_components[1], "Upper", var_components[2])
    varLower <- paste0(var_components[1], "Lower", var_components[2])
    if (varUpper %in% names(glb_models_df)) {
        warning(varUpper, " already exists in glb_models_df")
        # Assuming Lower also exists
        next
    }    
    print(sprintf("var:%s", var))
    # CI is dependent on sample size in t distribution; df=n-1
    glb_models_df[, varUpper] <- glb_models_df[, varActul] + 
        glb_models_df[, "min.sd2ci.scaler"] * glb_models_df[, var]
    glb_models_df[, varLower] <- glb_models_df[, varActul] - 
        glb_models_df[, "min.sd2ci.scaler"] * glb_models_df[, var]
}
## Warning: max.AccuracyUpper.fit already exists in glb_models_df
## [1] "var:max.KappaSD.fit"
# Plot metrics with CI
plt_models_df <- glb_models_df[, "model_id", FALSE]
pltCI_models_df <- glb_models_df[, "model_id", FALSE]
for (var in grep("Upper", names(glb_models_df), value=TRUE)) {
    var_components <- unlist(strsplit(var, "Upper"))
    col_name <- unlist(paste(var_components, collapse=""))
    plt_models_df[, col_name] <- glb_models_df[, col_name]
    for (name in paste0(var_components[1], c("Upper", "Lower"), var_components[2]))
        pltCI_models_df[, name] <- glb_models_df[, name]
}

build_statsCI_data <- function(plt_models_df) {
    mltd_models_df <- melt(plt_models_df, id.vars="model_id")
    mltd_models_df$data <- sapply(1:nrow(mltd_models_df), 
        function(row_ix) tail(unlist(strsplit(as.character(
            mltd_models_df[row_ix, "variable"]), "[.]")), 1))
    mltd_models_df$label <- sapply(1:nrow(mltd_models_df), 
        function(row_ix) head(unlist(strsplit(as.character(
            mltd_models_df[row_ix, "variable"]), 
            paste0(".", mltd_models_df[row_ix, "data"]))), 1))
    #print(mltd_models_df)
    
    return(mltd_models_df)
}
mltd_models_df <- build_statsCI_data(plt_models_df)

mltdCI_models_df <- melt(pltCI_models_df, id.vars="model_id")
for (row_ix in 1:nrow(mltdCI_models_df)) {
    for (type in c("Upper", "Lower")) {
        if (length(var_components <- unlist(strsplit(
                as.character(mltdCI_models_df[row_ix, "variable"]), type))) > 1) {
            #print(sprintf("row_ix:%d; type:%s; ", row_ix, type))
            mltdCI_models_df[row_ix, "label"] <- var_components[1]
            mltdCI_models_df[row_ix, "data"] <- 
                unlist(strsplit(var_components[2], "[.]"))[2]
            mltdCI_models_df[row_ix, "type"] <- type
            break
        }
    }    
}
wideCI_models_df <- reshape(subset(mltdCI_models_df, select=-variable), 
                            timevar="type", 
        idvar=setdiff(names(mltdCI_models_df), c("type", "value", "variable")), 
                            direction="wide")
#print(wideCI_models_df)
mrgdCI_models_df <- merge(wideCI_models_df, mltd_models_df, all.x=TRUE)
#print(mrgdCI_models_df)

# Merge stats back in if CIs don't exist
goback_vars <- c()
for (var in unique(mltd_models_df$label)) {
    for (type in unique(mltd_models_df$data)) {
        var_type <- paste0(var, ".", type)
        # if this data is already present, next
        if (var_type %in% unique(paste(mltd_models_df$label, mltd_models_df$data,
                                       sep=".")))
            next
        #print(sprintf("var_type:%s", var_type))
        goback_vars <- c(goback_vars, var_type)
    }
}

if (length(goback_vars) > 0) {
    mltd_goback_df <- build_statsCI_data(glb_models_df[, c("model_id", goback_vars)])
    mltd_models_df <- rbind(mltd_models_df, mltd_goback_df)
}

mltd_models_df <- merge(mltd_models_df, glb_models_df[, c("model_id", "model_method")], 
                        all.x=TRUE)

png(paste0(glb_out_pfx, "models_bar.png"), width=480*3, height=480*2)
print(gp <- myplot_bar(mltd_models_df, "model_id", "value", colorcol_name="model_method") + 
        geom_errorbar(data=mrgdCI_models_df, 
            mapping=aes(x=model_id, ymax=value.Upper, ymin=value.Lower), width=0.5) + 
          facet_grid(label ~ data, scales="free") + 
          theme(axis.text.x = element_text(angle = 90,vjust = 0.5)))
dev.off()
## quartz_off_screen 
##                 2
print(gp)

# used for console inspection
model_evl_terms <- c(NULL)
for (metric in glb_model_evl_criteria)
    model_evl_terms <- c(model_evl_terms, 
                         ifelse(length(grep("max", metric)) > 0, "-", "+"), metric)
if (glb_is_classification && glb_is_binomial)
    model_evl_terms <- c(model_evl_terms, "-", "opt.prob.threshold.OOB")
model_sel_frmla <- as.formula(paste(c("~ ", model_evl_terms), collapse=" "))
dsp_models_cols <- c("model_id", glb_model_evl_criteria) 
if (glb_is_classification && glb_is_binomial) 
    dsp_models_cols <- c(dsp_models_cols, "opt.prob.threshold.OOB")
print(dsp_models_df <- orderBy(model_sel_frmla, glb_models_df)[, dsp_models_cols])
##                     model_id max.Accuracy.OOB max.auc.OOB max.Kappa.OOB
## 7              Low.cor.X.glm        0.8910891   0.8938547     0.4799906
## 8                  All.X.glm        0.8910891   0.8938547     0.4799906
## 9             All.X.bayesglm        0.8861386   0.8945834     0.4660997
## 1          MFO.myMFO_classfr        0.8861386   0.5000000     0.0000000
## 3       Max.cor.Y.cv.0.rpart        0.8861386   0.5000000     0.0000000
## 5            Max.cor.Y.rpart        0.8861386   0.5000000     0.0000000
## 10      All.X.no.rnorm.rpart        0.8861386   0.5000000     0.0000000
## 6              Max.cor.Y.glm        0.8762376   0.8581491     0.4924623
## 4  Max.cor.Y.cv.0.cp.0.rpart        0.8762376   0.7951178     0.4924623
## 12                 Csm.1.glm        0.8663366   0.9023561     0.4989895
## 11         All.X.no.rnorm.rf        0.8564356   0.8796454     0.4459996
## 2    Random.myrandom_classfr        0.1138614   0.4602866     0.0000000
##    min.aic.fit opt.prob.threshold.OOB
## 7     279.4111                    0.5
## 8     279.4111                    0.5
## 9     279.5551                    0.4
## 1           NA                    0.5
## 3           NA                    0.5
## 5           NA                    0.5
## 10          NA                    0.5
## 6     288.5369                    0.3
## 4           NA                    0.3
## 12    270.5307                    0.2
## 11          NA                    0.3
## 2           NA                    0.1
print(myplot_radar(radar_inp_df=dsp_models_df))
## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors
## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.
## Warning: Removed 38 rows containing missing values (geom_point).
## Warning: Removed 7 rows containing missing values (geom_text).
## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors
## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 12. Consider specifying shapes manually if you must have them.

print("Metrics used for model selection:"); print(model_sel_frmla)
## [1] "Metrics used for model selection:"
## ~-max.Accuracy.OOB - max.auc.OOB - max.Kappa.OOB + min.aic.fit - 
##     opt.prob.threshold.OOB
print(sprintf("Best model id: %s", dsp_models_df[1, "model_id"]))
## [1] "Best model id: Low.cor.X.glm"
if (is.null(glb_sel_mdl_id)) { 
    glb_sel_mdl_id <- dsp_models_df[1, "model_id"]
#     if (glb_sel_mdl_id == "Interact.High.cor.Y.glm") {
#         warning("glb_sel_mdl_id: Interact.High.cor.Y.glm; myextract_mdl_feats does not currently support interaction terms")
#         glb_sel_mdl_id <- dsp_models_df[2, "model_id"]
#     }
} else 
    print(sprintf("User specified selection: %s", glb_sel_mdl_id))   
    
myprint_mdl(glb_sel_mdl <- glb_models_lst[[glb_sel_mdl_id]])

## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.7256  -0.4288  -0.2719  -0.1681   2.8478  
## 
## Coefficients:
##                     Estimate Std. Error z value Pr(>|z|)    
## (Intercept)       -4.2474963  1.2952911  -3.279  0.00104 ** 
## multiple.offenses  1.6254434  0.3886164   4.183 2.88e-05 ***
## race               0.8823506  0.3953679   2.232  0.02563 *  
## age               -0.0003604  0.0160915  -0.022  0.98213    
## male               0.3878796  0.4385200   0.885  0.37642    
## .rnorm             0.0474484  0.1748880   0.271  0.78615    
## crime.fctr2        0.6720975  0.5030137   1.336  0.18150    
## crime.fctr3       -0.2805264  0.4328933  -0.648  0.51697    
## crime.fctr4       -0.0036558  0.5717918  -0.006  0.99490    
## time.served       -0.1219743  0.1205154  -1.012  0.31149    
## max.sentence       0.0801944  0.0554146   1.447  0.14785    
## state.fctr2        0.4585050  0.4855775   0.944  0.34504    
## state.fctr3        0.8535218  0.5607749   1.522  0.12800    
## state.fctr4       -3.3945448  0.6115599  -5.551 2.85e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 251.41  on 459  degrees of freedom
## AIC: 279.41
## 
## Number of Fisher Scoring iterations: 6
## [1] TRUE
# From here to save(), this should all be in one function
#   these are executed in the same seq twice more:
#       fit.data.training & predict.data.new chunks
glb_get_predictions <- function(df, mdl_id, rsp_var_out, prob_threshold_def=NULL) {
    mdl <- glb_models_lst[[mdl_id]]
    rsp_var_out <- paste0(rsp_var_out, mdl_id)

    if (glb_is_regression) {
        df[, rsp_var_out] <- predict(mdl, newdata=df, type="raw")
        print(myplot_scatter(df, glb_rsp_var, rsp_var_out, smooth=TRUE))
        df[, paste0(rsp_var_out, ".err")] <- 
            abs(df[, rsp_var_out] - df[, glb_rsp_var])
        print(head(orderBy(reformulate(c("-", paste0(rsp_var_out, ".err"))), 
                           df)))                             
    }

    if (glb_is_classification && glb_is_binomial) {
        prob_threshold <- glb_models_df[glb_models_df$model_id == mdl_id, 
                                        "opt.prob.threshold.OOB"]
        if (is.null(prob_threshold) || is.na(prob_threshold)) {
            warning("Using default probability threshold: ", prob_threshold_def)
            if (is.null(prob_threshold <- prob_threshold_def))
                stop("Default probability threshold is NULL")
        }
        
        df[, paste0(rsp_var_out, ".prob")] <- 
            predict(mdl, newdata=df, type="prob")[, 2]
        df[, rsp_var_out] <- 
                factor(levels(df[, glb_rsp_var])[
                    (df[, paste0(rsp_var_out, ".prob")] >=
                        prob_threshold) * 1 + 1], levels(df[, glb_rsp_var]))
    
        # prediction stats already reported by myfit_mdl ???
    }    
    
    if (glb_is_classification && !glb_is_binomial) {
        df[, rsp_var_out] <- predict(mdl, newdata=df, type="raw")
        df[, paste0(rsp_var_out, ".prob")] <- 
            predict(mdl, newdata=df, type="prob")
    }

    return(df)
}    
glb_OOBobs_df <- glb_get_predictions(df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id, 
                                     rsp_var_out=glb_rsp_var_out)
predct_accurate_var_name <- paste0(glb_rsp_var_out, glb_sel_mdl_id, ".accurate")
glb_OOBobs_df[, predct_accurate_var_name] <-
                    (glb_OOBobs_df[, glb_rsp_var] == 
                     glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)])

#stop(here"); #sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df
glb_featsimp_df <- 
    myget_feats_importance(mdl=glb_sel_mdl, featsimp_df=NULL)
glb_featsimp_df[, paste0(glb_sel_mdl_id, ".importance")] <- glb_featsimp_df$importance
print(glb_featsimp_df)
##                   importance Low.cor.X.glm.importance
## state.fctr4       100.000000               100.000000
## multiple.offenses  75.325903                75.325903
## race               40.137639                40.137639
## state.fctr3        27.337315                27.337315
## max.sentence       25.986908                25.986908
## crime.fctr2        23.984318                23.984318
## time.served        18.139763                18.139763
## state.fctr2        16.915809                16.915809
## male               15.838533                15.838533
## crime.fctr3        11.572965                11.572965
## .rnorm              4.778184                 4.778184
## age                 0.288684                 0.288684
## crime.fctr4         0.000000                 0.000000
# Used again in fit.data.training & predict.data.new chunks
glb_analytics_diag_plots <- function(obs_df, mdl_id, prob_threshold=NULL) {
    featsimp_df <- glb_featsimp_df
    featsimp_df$feat <- gsub("`(.*?)`", "\\1", row.names(featsimp_df))    
    featsimp_df$feat.interact <- gsub("(.*?):(.*)", "\\2", featsimp_df$feat)
    featsimp_df$feat <- gsub("(.*?):(.*)", "\\1", featsimp_df$feat)    
    featsimp_df$feat.interact <- ifelse(featsimp_df$feat.interact == featsimp_df$feat, 
                                        NA, featsimp_df$feat.interact)
    featsimp_df$feat <- gsub("(.*?)\\.fctr(.*)", "\\1\\.fctr", featsimp_df$feat)
    featsimp_df$feat.interact <- gsub("(.*?)\\.fctr(.*)", "\\1\\.fctr", featsimp_df$feat.interact) 
    featsimp_df <- orderBy(~ -importance.max, summaryBy(importance ~ feat + feat.interact, 
                                                        data=featsimp_df, FUN=max))    
    #rex_str=":(.*)"; txt_vctr=tail(featsimp_df$feat); ret_lst <- regexec(rex_str, txt_vctr); ret_lst <- regmatches(txt_vctr, ret_lst); ret_vctr <- sapply(1:length(ret_lst), function(pos_ix) ifelse(length(ret_lst[[pos_ix]]) > 0, ret_lst[[pos_ix]], "")); print(ret_vctr <- ret_vctr[ret_vctr != ""])    
    if (nrow(featsimp_df) > 5) {
        warning("Limiting important feature scatter plots to 5 out of ", nrow(featsimp_df))
        featsimp_df <- head(featsimp_df, 5)
    }
    
#     if (!all(is.na(featsimp_df$feat.interact)))
#         stop("not implemented yet")
    rsp_var_out <- paste0(glb_rsp_var_out, mdl_id)
    for (var in featsimp_df$feat) {
        plot_df <- melt(obs_df, id.vars=var, 
                        measure.vars=c(glb_rsp_var, rsp_var_out))

#         if (var == "<feat_name>") print(myplot_scatter(plot_df, var, "value", 
#                                              facet_colcol_name="variable") + 
#                       geom_vline(xintercept=<divider_val>, linetype="dotted")) else     
            print(myplot_scatter(plot_df, var, "value", colorcol_name="variable",
                                 facet_colcol_name="variable", jitter=TRUE) + 
                      guides(color=FALSE))
    }
    
    if (glb_is_regression) {
        if (nrow(featsimp_df) == 0)
            warning("No important features in glb_fin_mdl") else
            print(myplot_prediction_regression(df=obs_df, 
                        feat_x=ifelse(nrow(featsimp_df) > 1, featsimp_df$feat[2],
                                      ".rownames"), 
                                               feat_y=featsimp_df$feat[1],
                        rsp_var=glb_rsp_var, rsp_var_out=rsp_var_out,
                        id_vars=glb_id_var)
    #               + facet_wrap(reformulate(featsimp_df$feat[2])) # if [1 or 2] is a factor
    #               + geom_point(aes_string(color="<col_name>.fctr")) #  to color the plot
                  )
    }    
    
    if (glb_is_classification) {
        if (nrow(featsimp_df) == 0)
            warning("No features in selected model are statistically important")
        else print(myplot_prediction_classification(df=obs_df, 
                feat_x=ifelse(nrow(featsimp_df) > 1, featsimp_df$feat[2], 
                              ".rownames"),
                                               feat_y=featsimp_df$feat[1],
                     rsp_var=glb_rsp_var, 
                     rsp_var_out=rsp_var_out, 
                     id_vars=glb_id_var,
                    prob_threshold=prob_threshold)
#               + geom_hline(yintercept=<divider_val>, linetype = "dotted")
                )
    }    
}
if (glb_is_classification && glb_is_binomial)
    glb_analytics_diag_plots(obs_df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id, 
            prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, 
                                         "opt.prob.threshold.OOB"]) else
    glb_analytics_diag_plots(obs_df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id)                  
## Warning in glb_analytics_diag_plots(obs_df = glb_OOBobs_df, mdl_id =
## glb_sel_mdl_id, : Limiting important feature scatter plots to 5 out of 9

## [1] "Min/Max Boundaries: "
##     .rownames violator.fctr violator.fctr.predict.Low.cor.X.glm.prob
## 81         81             Y                               0.08126855
## 269       269             Y                               0.09309703
## 219       219             Y                               0.12243097
## 257       257             Y                               0.19159960
## 130       130             Y                               0.20777500
## 10         10             N                               0.26038179
## 138       138             N                               0.42351984
## 141       141             N                               0.53915253
## 204       204             N                               0.54496939
## 192       192             N                               0.56944173
## 199       199             N                               0.57495379
## 201       201             N                               0.58093613
## 205       205             N                               0.58234150
##     violator.fctr.predict.Low.cor.X.glm
## 81                                    N
## 269                                   N
## 219                                   N
## 257                                   N
## 130                                   N
## 10                                    N
## 138                                   N
## 141                                   Y
## 204                                   Y
## 192                                   Y
## 199                                   Y
## 201                                   Y
## 205                                   Y
##     violator.fctr.predict.Low.cor.X.glm.accurate
## 81                                         FALSE
## 269                                        FALSE
## 219                                        FALSE
## 257                                        FALSE
## 130                                        FALSE
## 10                                          TRUE
## 138                                         TRUE
## 141                                        FALSE
## 204                                        FALSE
## 192                                        FALSE
## 199                                        FALSE
## 201                                        FALSE
## 205                                        FALSE
##     violator.fctr.predict.Low.cor.X.glm.error .label
## 81                                -0.41873145     81
## 269                               -0.40690297    269
## 219                               -0.37756903    219
## 257                               -0.30840040    257
## 130                               -0.29222500    130
## 10                                 0.00000000     10
## 138                                0.00000000    138
## 141                                0.03915253    141
## 204                                0.04496939    204
## 192                                0.06944173    192
## 199                                0.07495379    199
## 201                                0.08093613    201
## 205                                0.08234150    205
## [1] "Inaccurate: "
##     .rownames violator.fctr violator.fctr.predict.Low.cor.X.glm.prob
## 647       647             Y                               0.06838857
## 81         81             Y                               0.08126855
## 269       269             Y                               0.09309703
## 219       219             Y                               0.12243097
## 66         66             Y                               0.16952883
## 257       257             Y                               0.19159960
##     violator.fctr.predict.Low.cor.X.glm
## 647                                   N
## 81                                    N
## 269                                   N
## 219                                   N
## 66                                    N
## 257                                   N
##     violator.fctr.predict.Low.cor.X.glm.accurate
## 647                                        FALSE
## 81                                         FALSE
## 269                                        FALSE
## 219                                        FALSE
## 66                                         FALSE
## 257                                        FALSE
##     violator.fctr.predict.Low.cor.X.glm.error
## 647                                -0.4316114
## 81                                 -0.4187314
## 269                                -0.4069030
## 219                                -0.3775690
## 66                                 -0.3304712
## 257                                -0.3084004
##     .rownames violator.fctr violator.fctr.predict.Low.cor.X.glm.prob
## 647       647             Y                               0.06838857
## 51         51             Y                               0.28236865
## 47         47             Y                               0.28978035
## 208       208             N                               0.57157404
## 205       205             N                               0.58234150
## 216       216             N                               0.77017796
##     violator.fctr.predict.Low.cor.X.glm
## 647                                   N
## 51                                    N
## 47                                    N
## 208                                   Y
## 205                                   Y
## 216                                   Y
##     violator.fctr.predict.Low.cor.X.glm.accurate
## 647                                        FALSE
## 51                                         FALSE
## 47                                         FALSE
## 208                                        FALSE
## 205                                        FALSE
## 216                                        FALSE
##     violator.fctr.predict.Low.cor.X.glm.error
## 647                               -0.43161143
## 51                                -0.21763135
## 47                                -0.21021965
## 208                                0.07157404
## 205                                0.08234150
## 216                                0.27017796
##     .rownames violator.fctr violator.fctr.predict.Low.cor.X.glm.prob
## 201       201             N                                0.5809361
## 205       205             N                                0.5823415
## 226       226             N                                0.6993251
## 230       230             N                                0.7385133
## 216       216             N                                0.7701780
## 229       229             N                                0.8571941
##     violator.fctr.predict.Low.cor.X.glm
## 201                                   Y
## 205                                   Y
## 226                                   Y
## 230                                   Y
## 216                                   Y
## 229                                   Y
##     violator.fctr.predict.Low.cor.X.glm.accurate
## 201                                        FALSE
## 205                                        FALSE
## 226                                        FALSE
## 230                                        FALSE
## 216                                        FALSE
## 229                                        FALSE
##     violator.fctr.predict.Low.cor.X.glm.error
## 201                                0.08093613
## 205                                0.08234150
## 226                                0.19932507
## 230                                0.23851334
## 216                                0.27017796
## 229                                0.35719408

# gather predictions from models better than MFO.*
#mdl_id <- "Conditional.X.rf"
#mdl_id <- "Conditional.X.cp.0.rpart"
#mdl_id <- "Conditional.X.rpart"
# glb_OOBobs_df <- glb_get_predictions(df=glb_OOBobs_df, mdl_id,
#                                      glb_rsp_var_out)
# print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, mdl_id)], 
#                         glb_OOBobs_df[, glb_rsp_var])$table))
# FN_OOB_ids <- c(4721, 4020, 693, 92)
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                     grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                     glb_feats_df$id[1:5]])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                     glb_txt_vars])
write.csv(glb_OOBobs_df[, c(glb_id_var, 
                grep(glb_rsp_var, names(glb_OOBobs_df), fixed=TRUE, value=TRUE))], 
    paste0(gsub(".", "_", paste0(glb_out_pfx, glb_sel_mdl_id), fixed=TRUE), 
           "_OOBobs.csv"), row.names=FALSE)

# print(glb_allobs_df[glb_allobs_df$UniqueID %in% FN_OOB_ids, 
#                     glb_txt_vars])
# dsp_tbl(Headline.contains="[Ee]bola")
# sum(sel_obs(Headline.contains="[Ee]bola"))
# ftable(xtabs(Popular ~ NewsDesk.fctr, data=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,]))
# xtabs(NewsDesk ~ Popular, #Popular ~ NewsDesk.fctr, 
#       data=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,],
#       exclude=NULL)
# print(mycreate_xtab_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular", "NewsDesk", "SectionName", "SubsectionName")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular", "NewsDesk", "SectionName", "SubsectionName")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], 
#                       tbl_col_names=c("Popular", "NewsDesk")))

# write.csv(glb_chunks_df, paste0(glb_out_pfx, tail(glb_chunks_df, 1)$label, "_",
#                                 tail(glb_chunks_df, 1)$step_minor,  "_chunks1.csv"),
#           row.names=FALSE)

glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)
##         label step_major step_minor    bgn    end elapsed
## 12 fit.models          7          2 64.781 78.793  14.013
## 13 fit.models          7          3 78.794     NA      NA
print(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
## character(0)
print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))
## character(0)
print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
## [1] "violator.fctr.predict.Low.cor.X.glm.prob"    
## [2] "violator.fctr.predict.Low.cor.X.glm"         
## [3] "violator.fctr.predict.Low.cor.X.glm.accurate"
for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
    # Merge or cbind ?
    glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
    
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))
## character(0)
if (glb_save_envir)
    save(glb_feats_df, 
         glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
         glb_models_df, dsp_models_df, glb_models_lst, glb_sel_mdl, glb_sel_mdl_id,
         glb_model_type,
        file=paste0(glb_out_pfx, "selmdl_dsk.RData"))
#load(paste0(glb_out_pfx, "selmdl_dsk.RData"))

rm(ret_lst)
## Warning in rm(ret_lst): object 'ret_lst' not found
replay.petrisim(pn=glb_analytics_pn, 
    replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs, 
        "model.selected")), flip_coord=TRUE)
## time trans    "bgn " "fit.data.training.all " "predict.data.new " "end " 
## 0.0000   multiple enabled transitions:  data.training.all data.new model.selected    firing:  data.training.all 
## 1.0000    1   2 1 0 0 
## 1.0000   multiple enabled transitions:  data.training.all data.new model.selected model.final data.training.all.prediction   firing:  data.new 
## 2.0000    2   1 1 1 0 
## 2.0000   multiple enabled transitions:  data.training.all data.new model.selected model.final data.training.all.prediction data.new.prediction   firing:  model.selected 
## 3.0000    3   0 2 1 0

glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.data.training", major.inc=TRUE)
##                label step_major step_minor    bgn    end elapsed
## 13        fit.models          7          3 78.794 82.895   4.101
## 14 fit.data.training          8          0 82.896     NA      NA

Step 8.0: fit data training

#load(paste0(glb_inp_pfx, "dsk.RData"))

# To create specific models
# glb_fin_mdl_id <- NULL; glb_fin_mdl <- NULL; 
# glb_sel_mdl_id <- "Conditional.X.cp.0.rpart"; 
# glb_sel_mdl <- glb_models_lst[[glb_sel_mdl_id]]; print(glb_sel_mdl)
    
if (!is.null(glb_fin_mdl_id) && (glb_fin_mdl_id %in% names(glb_models_lst))) {
    warning("Final model same as user selected model")
    glb_fin_mdl <- glb_sel_mdl
} else {    
#     print(mdl_feats_df <- myextract_mdl_feats(sel_mdl=glb_sel_mdl, 
#                                               entity_df=glb_fitobs_df))
    
    if ((model_method <- glb_sel_mdl$method) == "custom")
        # get actual method from the model_id
        model_method <- tail(unlist(strsplit(glb_sel_mdl_id, "[.]")), 1)
        
    tune_finmdl_df <- NULL
    if (nrow(glb_sel_mdl$bestTune) > 0) {
        for (param in names(glb_sel_mdl$bestTune)) {
            #print(sprintf("param: %s", param))
            if (glb_sel_mdl$bestTune[1, param] != "none")
                tune_finmdl_df <- rbind(tune_finmdl_df, 
                    data.frame(parameter=param, 
                               min=glb_sel_mdl$bestTune[1, param], 
                               max=glb_sel_mdl$bestTune[1, param], 
                               by=1)) # by val does not matter
        }
    } 
    
    # Sync with parameters in mydsutils.R
    require(gdata)
    ret_lst <- myfit_mdl(model_id="Final", model_method=model_method,
        indep_vars_vctr=trim(unlist(strsplit(glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
                                                    "feats"], "[,]"))), 
                         model_type=glb_model_type,
                            rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out, 
                            fit_df=glb_trnobs_df, OOB_df=NULL,
                            n_cv_folds=glb_n_cv_folds, tune_models_df=tune_finmdl_df,
                         # Automate from here
                         #  Issues if glb_sel_mdl$method == "rf" b/c trainControl is "oob"; not "cv"
                            model_loss_mtrx=glb_model_metric_terms,
                            model_summaryFunction=glb_sel_mdl$control$summaryFunction,
                            model_metric=glb_sel_mdl$metric,
                            model_metric_maximize=glb_sel_mdl$maximize)
    glb_fin_mdl <- glb_models_lst[[length(glb_models_lst)]] 
    glb_fin_mdl_id <- glb_models_df[length(glb_models_lst), "model_id"]
}
## Loading required package: gdata
## gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
## 
## gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
## 
## Attaching package: 'gdata'
## 
## The following object is masked from 'package:randomForest':
## 
##     combine
## 
## The following objects are masked from 'package:dplyr':
## 
##     combine, first, last
## 
## The following object is masked from 'package:stats':
## 
##     nobs
## 
## The following object is masked from 'package:utils':
## 
##     object.size
## [1] "fitting model: Final.glm"
## [1] "    indep_vars: multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr"
## Aggregating results
## Fitting final model on full training set

## 
## Call:
## NULL
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.7256  -0.4288  -0.2719  -0.1681   2.8478  
## 
## Coefficients:
##                     Estimate Std. Error z value Pr(>|z|)    
## (Intercept)       -4.2474963  1.2952911  -3.279  0.00104 ** 
## multiple.offenses  1.6254434  0.3886164   4.183 2.88e-05 ***
## race               0.8823506  0.3953679   2.232  0.02563 *  
## age               -0.0003604  0.0160915  -0.022  0.98213    
## male               0.3878796  0.4385200   0.885  0.37642    
## .rnorm             0.0474484  0.1748880   0.271  0.78615    
## crime.fctr2        0.6720975  0.5030137   1.336  0.18150    
## crime.fctr3       -0.2805264  0.4328933  -0.648  0.51697    
## crime.fctr4       -0.0036558  0.5717918  -0.006  0.99490    
## time.served       -0.1219743  0.1205154  -1.012  0.31149    
## max.sentence       0.0801944  0.0554146   1.447  0.14785    
## state.fctr2        0.4585050  0.4855775   0.944  0.34504    
## state.fctr3        0.8535218  0.5607749   1.522  0.12800    
## state.fctr4       -3.3945448  0.6115599  -5.551 2.85e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 340.04  on 472  degrees of freedom
## Residual deviance: 251.41  on 459  degrees of freedom
## AIC: 279.41
## 
## Number of Fisher Scoring iterations: 6
## 
## [1] "    calling mypredict_mdl for fit:"

##    threshold   f.score
## 1        0.0 0.2083333
## 2        0.1 0.4081633
## 3        0.2 0.4822695
## 4        0.3 0.4705882
## 5        0.4 0.4565217
## 6        0.5 0.4102564
## 7        0.6 0.2941176
## 8        0.7 0.2187500
## 9        0.8 0.1034483
## 10       0.9 0.0000000
## 11       1.0 0.0000000
## [1] "Classifier Probability Threshold: 0.2000 to maximize f.score.fit"
##   violator.fctr violator.fctr.predict.Final.glm.N
## 1             N                               366
## 2             Y                                21
##   violator.fctr.predict.Final.glm.Y
## 1                                52
## 2                                34
##          Prediction
## Reference   N   Y
##         N 366  52
##         Y  21  34
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##   0.8456659619   0.3966942149   0.8099028745   0.8770336126   0.8837209302 
## AccuracyPValue  McnemarPValue 
##   0.9947311468   0.0004460309
## Warning in mypredict_mdl(mdl, df = fit_df, rsp_var, rsp_var_out,
## model_id_method, : Expecting 1 metric: Accuracy; recd: Accuracy, Kappa;
## retaining Accuracy only

##    model_id model_method
## 1 Final.glm          glm
##                                                                                           feats
## 1 multiple.offenses, race, age, male, .rnorm, crime.fctr, time.served, max.sentence, state.fctr
##   max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1               1                      0.971                 0.013
##   max.auc.fit opt.prob.threshold.fit max.f.score.fit max.Accuracy.fit
## 1    0.845759                    0.2       0.4822695         0.879505
##   max.AccuracyLower.fit max.AccuracyUpper.fit max.Kappa.fit min.aic.fit
## 1             0.8099029             0.8770336     0.2015256    279.4111
##   max.AccuracySD.fit max.KappaSD.fit
## 1        0.005969975      0.07399248
rm(ret_lst)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.data.training", major.inc=FALSE)
##                label step_major step_minor    bgn    end elapsed
## 14 fit.data.training          8          0 82.896 87.581   4.685
## 15 fit.data.training          8          1 87.582     NA      NA
glb_trnobs_df <- glb_get_predictions(df=glb_trnobs_df, mdl_id=glb_fin_mdl_id, 
                                     rsp_var_out=glb_rsp_var_out,
    prob_threshold_def=ifelse(glb_is_classification && glb_is_binomial, 
        glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, "opt.prob.threshold.OOB"], NULL))
## Warning in glb_get_predictions(df = glb_trnobs_df, mdl_id =
## glb_fin_mdl_id, : Using default probability threshold: 0.5
sav_featsimp_df <- glb_featsimp_df
#glb_feats_df <- sav_feats_df
# glb_feats_df <- mymerge_feats_importance(feats_df=glb_feats_df, sel_mdl=glb_fin_mdl, 
#                                                entity_df=glb_trnobs_df)
glb_featsimp_df <- myget_feats_importance(mdl=glb_fin_mdl, featsimp_df=glb_featsimp_df)
glb_featsimp_df[, paste0(glb_fin_mdl_id, ".importance")] <- glb_featsimp_df$importance
print(glb_featsimp_df)
##                   Low.cor.X.glm.importance importance Final.glm.importance
## state.fctr4                     100.000000 100.000000           100.000000
## multiple.offenses                75.325903  75.325903            75.325903
## race                             40.137639  40.137639            40.137639
## state.fctr3                      27.337315  27.337315            27.337315
## max.sentence                     25.986908  25.986908            25.986908
## crime.fctr2                      23.984318  23.984318            23.984318
## time.served                      18.139763  18.139763            18.139763
## state.fctr2                      16.915809  16.915809            16.915809
## male                             15.838533  15.838533            15.838533
## crime.fctr3                      11.572965  11.572965            11.572965
## .rnorm                            4.778184   4.778184             4.778184
## age                               0.288684   0.288684             0.288684
## crime.fctr4                       0.000000   0.000000             0.000000
if (glb_is_classification && glb_is_binomial)
    glb_analytics_diag_plots(obs_df=glb_trnobs_df, mdl_id=glb_fin_mdl_id, 
            prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, 
                                         "opt.prob.threshold.OOB"]) else
    glb_analytics_diag_plots(obs_df=glb_trnobs_df, mdl_id=glb_fin_mdl_id)                  
## Warning in glb_analytics_diag_plots(obs_df = glb_trnobs_df, mdl_id =
## glb_fin_mdl_id, : Limiting important feature scatter plots to 5 out of 9

## [1] "Min/Max Boundaries: "
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 155       155             Y                           0.06569321
## 144       144             Y                           0.07392118
## 170       170             Y                           0.07928216
## 150       150             Y                           0.09731981
## 139       139             Y                           0.13110751
## 154       154             Y                           0.18152745
## 212       212             Y                           0.42398144
## 207       207             Y                           0.43516616
## 233       233             Y                           0.47262779
## 1           1             N                           0.09877782
## 11         11             N                           0.39144089
## 225       225             N                           0.57245974
## 237       237             N                           0.62129730
## 189       189             N                           0.77435233
##     violator.fctr.predict.Final.glm
## 155                               N
## 144                               N
## 170                               N
## 150                               N
## 139                               N
## 154                               N
## 212                               N
## 207                               N
## 233                               N
## 1                                 N
## 11                                N
## 225                               Y
## 237                               Y
## 189                               Y
##     violator.fctr.predict.Final.glm.accurate
## 155                                    FALSE
## 144                                    FALSE
## 170                                    FALSE
## 150                                    FALSE
## 139                                    FALSE
## 154                                    FALSE
## 212                                    FALSE
## 207                                    FALSE
## 233                                    FALSE
## 1                                       TRUE
## 11                                      TRUE
## 225                                    FALSE
## 237                                    FALSE
## 189                                    FALSE
##     violator.fctr.predict.Final.glm.error .label
## 155                           -0.43430679    155
## 144                           -0.42607882    144
## 170                           -0.42071784    170
## 150                           -0.40268019    150
## 139                           -0.36889249    139
## 154                           -0.31847255    154
## 212                           -0.07601856    212
## 207                           -0.06483384    207
## 233                           -0.02737221    233
## 1                              0.00000000      1
## 11                             0.00000000     11
## 225                            0.07245974    225
## 237                            0.12129730    237
## 189                            0.27435233    189
## [1] "Inaccurate: "
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 565       565             Y                           0.01733507
## 659       659             Y                           0.01925931
## 599       599             Y                           0.04161207
## 598       598             Y                           0.04225795
## 305       305             Y                           0.04862462
## 404       404             Y                           0.05311715
##     violator.fctr.predict.Final.glm
## 565                               N
## 659                               N
## 599                               N
## 598                               N
## 305                               N
## 404                               N
##     violator.fctr.predict.Final.glm.accurate
## 565                                    FALSE
## 659                                    FALSE
## 599                                    FALSE
## 598                                    FALSE
## 305                                    FALSE
## 404                                    FALSE
##     violator.fctr.predict.Final.glm.error
## 565                            -0.4826649
## 659                            -0.4807407
## 599                            -0.4583879
## 598                            -0.4577420
## 305                            -0.4513754
## 404                            -0.4468828
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 659       659             Y                           0.01925931
## 599       599             Y                           0.04161207
## 91         91             Y                           0.40455939
## 212       212             Y                           0.42398144
## 54         54             N                           0.52692362
## 243       243             N                           0.57903438
##     violator.fctr.predict.Final.glm
## 659                               N
## 599                               N
## 91                                N
## 212                               N
## 54                                Y
## 243                               Y
##     violator.fctr.predict.Final.glm.accurate
## 659                                    FALSE
## 599                                    FALSE
## 91                                     FALSE
## 212                                    FALSE
## 54                                     FALSE
## 243                                    FALSE
##     violator.fctr.predict.Final.glm.error
## 659                           -0.48074069
## 599                           -0.45838793
## 91                            -0.09544061
## 212                           -0.07601856
## 54                             0.02692362
## 243                            0.07903438
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 238       238             N                            0.5653227
## 225       225             N                            0.5724597
## 243       243             N                            0.5790344
## 237       237             N                            0.6212973
## 245       245             N                            0.7007789
## 189       189             N                            0.7743523
##     violator.fctr.predict.Final.glm
## 238                               Y
## 225                               Y
## 243                               Y
## 237                               Y
## 245                               Y
## 189                               Y
##     violator.fctr.predict.Final.glm.accurate
## 238                                    FALSE
## 225                                    FALSE
## 243                                    FALSE
## 237                                    FALSE
## 245                                    FALSE
## 189                                    FALSE
##     violator.fctr.predict.Final.glm.error
## 238                            0.06532270
## 225                            0.07245974
## 243                            0.07903438
## 237                            0.12129730
## 245                            0.20077888
## 189                            0.27435233

dsp_feats_vctr <- c(NULL)
for(var in grep(".importance", names(glb_feats_df), fixed=TRUE, value=TRUE))
    dsp_feats_vctr <- union(dsp_feats_vctr, 
                            glb_feats_df[!is.na(glb_feats_df[, var]), "id"])

# print(glb_trnobs_df[glb_trnobs_df$UniqueID %in% FN_OOB_ids, 
#                     grep(glb_rsp_var, names(glb_trnobs_df), value=TRUE)])

print(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
## [1] "violator.fctr.predict.Final.glm.prob"
## [2] "violator.fctr.predict.Final.glm"
for (col in setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
    # Merge or cbind ?
    glb_allobs_df[glb_allobs_df$.src == "Train", col] <- glb_trnobs_df[, col]

print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))
## character(0)
print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
## character(0)
for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
    # Merge or cbind ?
    glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
    
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))
## character(0)
if (glb_save_envir)
    save(glb_feats_df, glb_allobs_df, 
         #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
         glb_models_df, dsp_models_df, glb_models_lst, glb_model_type,
         glb_sel_mdl, glb_sel_mdl_id,
         glb_fin_mdl, glb_fin_mdl_id,
        file=paste0(glb_out_pfx, "dsk.RData"))

replay.petrisim(pn=glb_analytics_pn, 
    replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs, 
        "data.training.all.prediction","model.final")), flip_coord=TRUE)
## time trans    "bgn " "fit.data.training.all " "predict.data.new " "end " 
## 0.0000   multiple enabled transitions:  data.training.all data.new model.selected    firing:  data.training.all 
## 1.0000    1   2 1 0 0 
## 1.0000   multiple enabled transitions:  data.training.all data.new model.selected model.final data.training.all.prediction   firing:  data.new 
## 2.0000    2   1 1 1 0 
## 2.0000   multiple enabled transitions:  data.training.all data.new model.selected model.final data.training.all.prediction data.new.prediction   firing:  model.selected 
## 3.0000    3   0 2 1 0 
## 3.0000   multiple enabled transitions:  model.final data.training.all.prediction data.new.prediction     firing:  data.training.all.prediction 
## 4.0000    5   0 1 1 1 
## 4.0000   multiple enabled transitions:  model.final data.training.all.prediction data.new.prediction     firing:  model.final 
## 5.0000    4   0 0 2 1

glb_chunks_df <- myadd_chunk(glb_chunks_df, "predict.data.new", major.inc=TRUE)
##                label step_major step_minor    bgn    end elapsed
## 15 fit.data.training          8          1 87.582 92.339   4.758
## 16  predict.data.new          9          0 92.340     NA      NA

Step 9.0: predict data new

# Compute final model predictions
# sav_newobs_df <- glb_newobs_df
glb_newobs_df <- glb_get_predictions(glb_newobs_df, mdl_id=glb_fin_mdl_id, 
                                     rsp_var_out=glb_rsp_var_out,
    prob_threshold_def=ifelse(glb_is_classification && glb_is_binomial, 
        glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, 
                      "opt.prob.threshold.OOB"], NULL))
## Warning in glb_get_predictions(glb_newobs_df, mdl_id = glb_fin_mdl_id,
## rsp_var_out = glb_rsp_var_out, : Using default probability threshold: 0.5
if (glb_is_classification && glb_is_binomial)
    glb_analytics_diag_plots(obs_df=glb_newobs_df, mdl_id=glb_fin_mdl_id, 
            prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, 
                                         "opt.prob.threshold.OOB"]) else
    glb_analytics_diag_plots(obs_df=glb_newobs_df, mdl_id=glb_fin_mdl_id)                  
## Warning in glb_analytics_diag_plots(obs_df = glb_newobs_df, mdl_id =
## glb_fin_mdl_id, : Limiting important feature scatter plots to 5 out of 9

## [1] "Min/Max Boundaries: "
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 81         81             Y                           0.08126855
## 269       269             Y                           0.09309703
## 219       219             Y                           0.12243097
## 257       257             Y                           0.19159960
## 130       130             Y                           0.20777500
## 10         10             N                           0.26038179
## 138       138             N                           0.42351984
## 141       141             N                           0.53915253
## 204       204             N                           0.54496939
## 192       192             N                           0.56944173
## 199       199             N                           0.57495379
## 201       201             N                           0.58093613
## 205       205             N                           0.58234150
##     violator.fctr.predict.Final.glm
## 81                                N
## 269                               N
## 219                               N
## 257                               N
## 130                               N
## 10                                N
## 138                               N
## 141                               Y
## 204                               Y
## 192                               Y
## 199                               Y
## 201                               Y
## 205                               Y
##     violator.fctr.predict.Final.glm.accurate
## 81                                     FALSE
## 269                                    FALSE
## 219                                    FALSE
## 257                                    FALSE
## 130                                    FALSE
## 10                                      TRUE
## 138                                     TRUE
## 141                                    FALSE
## 204                                    FALSE
## 192                                    FALSE
## 199                                    FALSE
## 201                                    FALSE
## 205                                    FALSE
##     violator.fctr.predict.Final.glm.error .label
## 81                            -0.41873145     81
## 269                           -0.40690297    269
## 219                           -0.37756903    219
## 257                           -0.30840040    257
## 130                           -0.29222500    130
## 10                             0.00000000     10
## 138                            0.00000000    138
## 141                            0.03915253    141
## 204                            0.04496939    204
## 192                            0.06944173    192
## 199                            0.07495379    199
## 201                            0.08093613    201
## 205                            0.08234150    205
## [1] "Inaccurate: "
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 647       647             Y                           0.06838857
## 81         81             Y                           0.08126855
## 269       269             Y                           0.09309703
## 219       219             Y                           0.12243097
## 66         66             Y                           0.16952883
## 257       257             Y                           0.19159960
##     violator.fctr.predict.Final.glm
## 647                               N
## 81                                N
## 269                               N
## 219                               N
## 66                                N
## 257                               N
##     violator.fctr.predict.Final.glm.accurate
## 647                                    FALSE
## 81                                     FALSE
## 269                                    FALSE
## 219                                    FALSE
## 66                                     FALSE
## 257                                    FALSE
##     violator.fctr.predict.Final.glm.error
## 647                            -0.4316114
## 81                             -0.4187314
## 269                            -0.4069030
## 219                            -0.3775690
## 66                             -0.3304712
## 257                            -0.3084004
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 647       647             Y                           0.06838857
## 219       219             Y                           0.12243097
## 60         60             N                           0.50922399
## 208       208             N                           0.57157404
## 199       199             N                           0.57495379
## 226       226             N                           0.69932507
##     violator.fctr.predict.Final.glm
## 647                               N
## 219                               N
## 60                                Y
## 208                               Y
## 199                               Y
## 226                               Y
##     violator.fctr.predict.Final.glm.accurate
## 647                                    FALSE
## 219                                    FALSE
## 60                                     FALSE
## 208                                    FALSE
## 199                                    FALSE
## 226                                    FALSE
##     violator.fctr.predict.Final.glm.error
## 647                           -0.43161143
## 219                           -0.37756903
## 60                             0.00922399
## 208                            0.07157404
## 199                            0.07495379
## 226                            0.19932507
##     .rownames violator.fctr violator.fctr.predict.Final.glm.prob
## 201       201             N                            0.5809361
## 205       205             N                            0.5823415
## 226       226             N                            0.6993251
## 230       230             N                            0.7385133
## 216       216             N                            0.7701780
## 229       229             N                            0.8571941
##     violator.fctr.predict.Final.glm
## 201                               Y
## 205                               Y
## 226                               Y
## 230                               Y
## 216                               Y
## 229                               Y
##     violator.fctr.predict.Final.glm.accurate
## 201                                    FALSE
## 205                                    FALSE
## 226                                    FALSE
## 230                                    FALSE
## 216                                    FALSE
## 229                                    FALSE
##     violator.fctr.predict.Final.glm.error
## 201                            0.08093613
## 205                            0.08234150
## 226                            0.19932507
## 230                            0.23851334
## 216                            0.27017796
## 229                            0.35719408

if (glb_is_classification && glb_is_binomial) {
    submit_df <- glb_newobs_df[, c(glb_id_var, 
                                   paste0(glb_rsp_var_out, glb_fin_mdl_id, ".prob"))]
    names(submit_df)[2] <- "Probability1"
#     submit_df <- glb_newobs_df[, c(paste0(glb_rsp_var_out, glb_fin_mdl_id)), FALSE]
#     names(submit_df)[1] <- "BDscience"
#     submit_df$BDscience <- as.numeric(submit_df$BDscience) - 1
#     #submit_df <-rbind(submit_df, data.frame(bdanalytics=c(" ")))
#     print("Submission Stats:")
#     print(table(submit_df$BDscience, useNA = "ifany"))
} else submit_df <- glb_newobs_df[, c(glb_id_var, 
                                   paste0(glb_rsp_var_out, glb_fin_mdl_id))]
submit_fname <- paste0(gsub(".", "_", paste0(glb_out_pfx, glb_fin_mdl_id), fixed=TRUE), 
                    "_submit.csv")
write.csv(submit_df, submit_fname, quote=FALSE, row.names=FALSE)
#cat(" ", "\n", file=submit_fn, append=TRUE)

# print(orderBy(~ -max.auc.OOB, glb_models_df[, c("model_id", 
#             "max.auc.OOB", "max.Accuracy.OOB")]))
if (glb_is_classification && glb_is_binomial)
    print(glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, 
                        "opt.prob.threshold.OOB"])
## [1] 0.5
print(sprintf("glb_sel_mdl_id: %s", glb_sel_mdl_id))
## [1] "glb_sel_mdl_id: Low.cor.X.glm"
print(sprintf("glb_fin_mdl_id: %s", glb_fin_mdl_id))
## [1] "glb_fin_mdl_id: Final.glm"
print(dim(glb_fitobs_df))
## [1] 473  15
print(dsp_models_df)
##                     model_id max.Accuracy.OOB max.auc.OOB max.Kappa.OOB
## 7              Low.cor.X.glm        0.8910891   0.8938547     0.4799906
## 8                  All.X.glm        0.8910891   0.8938547     0.4799906
## 9             All.X.bayesglm        0.8861386   0.8945834     0.4660997
## 1          MFO.myMFO_classfr        0.8861386   0.5000000     0.0000000
## 3       Max.cor.Y.cv.0.rpart        0.8861386   0.5000000     0.0000000
## 5            Max.cor.Y.rpart        0.8861386   0.5000000     0.0000000
## 10      All.X.no.rnorm.rpart        0.8861386   0.5000000     0.0000000
## 6              Max.cor.Y.glm        0.8762376   0.8581491     0.4924623
## 4  Max.cor.Y.cv.0.cp.0.rpart        0.8762376   0.7951178     0.4924623
## 12                 Csm.1.glm        0.8663366   0.9023561     0.4989895
## 11         All.X.no.rnorm.rf        0.8564356   0.8796454     0.4459996
## 2    Random.myrandom_classfr        0.1138614   0.4602866     0.0000000
##    min.aic.fit opt.prob.threshold.OOB
## 7     279.4111                    0.5
## 8     279.4111                    0.5
## 9     279.5551                    0.4
## 1           NA                    0.5
## 3           NA                    0.5
## 5           NA                    0.5
## 10          NA                    0.5
## 6     288.5369                    0.3
## 4           NA                    0.3
## 12    270.5307                    0.2
## 11          NA                    0.3
## 2           NA                    0.1
if (glb_is_regression) {
    print(sprintf("%s OOB RMSE: %0.4f", glb_sel_mdl_id,
                  glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, "min.RMSE.OOB"]))

    if (!is.null(glb_category_vars)) {
        stop("not implemented yet")
        tmp_OOBobs_df <- glb_OOBobs_df[, c(glb_category_vars, predct_accurate_var_name)]
        names(tmp_OOBobs_df)[length(names(tmp_OOBobs_df))] <- "accurate.OOB"
        aOOB_ctgry_df <- mycreate_xtab_df(tmp_OOBobs_df, names(tmp_OOBobs_df)) 
        aOOB_ctgry_df[is.na(aOOB_ctgry_df)] <- 0
        aOOB_ctgry_df <- mutate(aOOB_ctgry_df, 
                                .n.OOB = accurate.OOB.FALSE + accurate.OOB.TRUE,
                                max.accuracy.OOB = accurate.OOB.TRUE / .n.OOB)
        #intersect(names(glb_ctgry_df), names(aOOB_ctgry_df))
        glb_ctgry_df <- merge(glb_ctgry_df, aOOB_ctgry_df, all=TRUE)
        print(orderBy(~-accurate.OOB.FALSE, glb_ctgry_df))
    }
    
    if ((glb_rsp_var %in% names(glb_newobs_df)) &&
        !(any(is.na(glb_newobs_df[, glb_rsp_var])))) {
            pred_stats_df <- 
                mypredict_mdl(mdl=glb_models_lst[[glb_fin_mdl_id]], 
                              df=glb_newobs_df, 
                              rsp_var=glb_rsp_var, 
                              rsp_var_out=glb_rsp_var_out, 
                              model_id_method=glb_fin_mdl_id, 
                              label="new",
                              model_summaryFunction=glb_sel_mdl$control$summaryFunction, 
                              model_metric=glb_sel_mdl$metric,
                              model_metric_maximize=glb_sel_mdl$maximize,
                              ret_type="stats")        
            print(sprintf("%s prediction stats for glb_newobs_df:", glb_fin_mdl_id))
            print(pred_stats_df)
    }    
}    
if (glb_is_classification) {
    print(sprintf("%s OOB confusion matrix & accuracy: ", glb_sel_mdl_id))
    print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)], 
                            glb_OOBobs_df[, glb_rsp_var])$table))

    if (!is.null(glb_category_vars)) {
        tmp_OOBobs_df <- glb_OOBobs_df[, c(glb_category_vars, predct_accurate_var_name)]
        names(tmp_OOBobs_df)[length(names(tmp_OOBobs_df))] <- "accurate.OOB"
        aOOB_ctgry_df <- mycreate_xtab_df(tmp_OOBobs_df, names(tmp_OOBobs_df)) 
        aOOB_ctgry_df[is.na(aOOB_ctgry_df)] <- 0
        aOOB_ctgry_df <- mutate(aOOB_ctgry_df, 
                                .n.OOB = accurate.OOB.FALSE + accurate.OOB.TRUE,
                                max.accuracy.OOB = accurate.OOB.TRUE / .n.OOB)
        #intersect(names(glb_ctgry_df), names(aOOB_ctgry_df))
        glb_ctgry_df <- merge(glb_ctgry_df, aOOB_ctgry_df, all=TRUE)
        print(orderBy(~-accurate.OOB.FALSE, glb_ctgry_df))
    }
    
    if ((glb_rsp_var %in% names(glb_newobs_df)) &&
        !(any(is.na(glb_newobs_df[, glb_rsp_var])))) {
        print(sprintf("%s new confusion matrix & accuracy: ", glb_fin_mdl_id))
        print(t(confusionMatrix(glb_newobs_df[, paste0(glb_rsp_var_out, glb_fin_mdl_id)], 
                                glb_newobs_df[, glb_rsp_var])$table))
    }    

}    
## [1] "Low.cor.X.glm OOB confusion matrix & accuracy: "
##          Prediction
## Reference   N   Y
##         N 167  12
##         Y  10  13
## [1] "Final.glm new confusion matrix & accuracy: "
##          Prediction
## Reference   N   Y
##         N 167  12
##         Y  10  13
dsp_myCategory_conf_mtrx <- function(myCategory) {
    print(sprintf("%s OOB::myCategory=%s confusion matrix & accuracy: ", 
                  glb_sel_mdl_id, myCategory))
    print(t(confusionMatrix(
        glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, 
                      paste0(glb_rsp_var_out, glb_sel_mdl_id)], 
        glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, glb_rsp_var])$table))
    print(sum(glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, 
                            predct_accurate_var_name]) / 
         nrow(glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, ]))
    err_ids <- glb_OOBobs_df[(glb_OOBobs_df$myCategory == myCategory) & 
                             (!glb_OOBobs_df[, predct_accurate_var_name]), glb_id_var]

    OOB_FNerr_df <- glb_OOBobs_df[(glb_OOBobs_df$UniqueID %in% err_ids) & 
                               (glb_OOBobs_df$Popular == 1), 
                        c(
                            ".clusterid", 
                            "Popular", "Headline", "Snippet", "Abstract")]
    print(sprintf("%s OOB::myCategory=%s FN errors: %d", glb_sel_mdl_id, myCategory,
                  nrow(OOB_FNerr_df)))
    print(OOB_FNerr_df)

    OOB_FPerr_df <- glb_OOBobs_df[(glb_OOBobs_df$UniqueID %in% err_ids) & 
                               (glb_OOBobs_df$Popular == 0), 
                        c(
                            ".clusterid", 
                            "Popular", "Headline", "Snippet", "Abstract")]
    print(sprintf("%s OOB::myCategory=%s FP errors: %d", glb_sel_mdl_id, myCategory,
                  nrow(OOB_FPerr_df)))
    print(OOB_FPerr_df)
}
#dsp_myCategory_conf_mtrx(myCategory="OpEd#Opinion#")
#dsp_myCategory_conf_mtrx(myCategory="Business#Business Day#Dealbook")
#dsp_myCategory_conf_mtrx(myCategory="##")

# if (glb_is_classification) {
#     print("FN_OOB_ids:")
#     print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                         grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
#     print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                         glb_txt_vars])
#     print(dsp_vctr <- colSums(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                         setdiff(grep("[HSA].", names(glb_OOBobs_df), value=TRUE),
#                                 union(myfind_chr_cols_df(glb_OOBobs_df),
#                     grep(".fctr", names(glb_OOBobs_df), fixed=TRUE, value=TRUE)))]))
# }

dsp_hdlpfx_results <- function(hdlpfx) {
    print(hdlpfx)
    print(glb_OOBobs_df[glb_OOBobs_df$Headline.pfx %in% c(hdlpfx), 
                        grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
    print(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx), 
                        grep(glb_rsp_var, names(glb_newobs_df), value=TRUE)])
    print(dsp_vctr <- colSums(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx), 
                        setdiff(grep("[HSA]\\.", names(glb_newobs_df), value=TRUE),
                                union(myfind_chr_cols_df(glb_newobs_df),
                    grep(".fctr", names(glb_newobs_df), fixed=TRUE, value=TRUE)))]))
    print(dsp_vctr <- dsp_vctr[dsp_vctr != 0])
    print(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx), 
                        union(names(dsp_vctr), myfind_chr_cols_df(glb_newobs_df))])
}
#dsp_hdlpfx_results(hdlpfx="Ask Well::")

# print("myMisc::|OpEd|blank|blank|1:")
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% c(6446), 
#                     grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])

# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids, 
#                     c("WordCount", "WordCount.log", "myMultimedia",
#                       "NewsDesk", "SectionName", "SubsectionName")])
# print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains="[Vv]ideo"), ], 
#                           c(glb_rsp_var, "myMultimedia")))
# dsp_chisq.test(Headline.contains="[Vi]deo")
# print(glb_allobs_df[sel_obs(Headline.contains="[Vv]ideo"), 
#                           c(glb_rsp_var, "Popular", "myMultimedia", "Headline")])
# print(glb_allobs_df[sel_obs(Headline.contains="[Ee]bola", Popular=1), 
#                           c(glb_rsp_var, "Popular", "myMultimedia", "Headline",
#                             "NewsDesk", "SectionName", "SubsectionName")])
# print(subset(glb_feats_df, !is.na(importance))[,
#     c("is.ConditionalX.y", 
#       grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, is.ConditionalX.y & is.na(importance))[,
#     c("is.ConditionalX.y", 
#       grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, !is.na(importance))[,
#     c("zeroVar", "nzv", "myNearZV", 
#       grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, is.na(importance))[,
#     c("zeroVar", "nzv", "myNearZV", 
#       grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
print(orderBy(as.formula(paste0("~ -", glb_sel_mdl_id, ".importance")), glb_featsimp_df))
##                   Low.cor.X.glm.importance importance Final.glm.importance
## state.fctr4                     100.000000 100.000000           100.000000
## multiple.offenses                75.325903  75.325903            75.325903
## race                             40.137639  40.137639            40.137639
## state.fctr3                      27.337315  27.337315            27.337315
## max.sentence                     25.986908  25.986908            25.986908
## crime.fctr2                      23.984318  23.984318            23.984318
## time.served                      18.139763  18.139763            18.139763
## state.fctr2                      16.915809  16.915809            16.915809
## male                             15.838533  15.838533            15.838533
## crime.fctr3                      11.572965  11.572965            11.572965
## .rnorm                            4.778184   4.778184             4.778184
## age                               0.288684   0.288684             0.288684
## crime.fctr4                       0.000000   0.000000             0.000000
# players_df <- data.frame(id=c("Chavez", "Giambi", "Menechino", "Myers", "Pena"),
#                          OBP=c(0.338, 0.391, 0.369, 0.313, 0.361),
#                          SLG=c(0.540, 0.450, 0.374, 0.447, 0.500),
#                         cost=c(1400000, 1065000, 295000, 800000, 300000))
# players_df$RS.predict <- predict(glb_models_lst[[csm_mdl_id]], players_df)
# print(orderBy(~ -RS.predict, players_df))

if (length(diff <- setdiff(names(glb_trnobs_df), names(glb_allobs_df))) > 0)   
    print(diff)
for (col in setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
    # Merge or cbind ?
    glb_allobs_df[glb_allobs_df$.src == "Train", col] <- glb_trnobs_df[, col]

if (length(diff <- setdiff(names(glb_fitobs_df), names(glb_allobs_df))) > 0)   
    print(diff)
if (length(diff <- setdiff(names(glb_OOBobs_df), names(glb_allobs_df))) > 0)   
    print(diff)

for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
    # Merge or cbind ?
    glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
    
if (length(diff <- setdiff(names(glb_newobs_df), names(glb_allobs_df))) > 0)   
    print(diff)

if (glb_save_envir)
    save(glb_feats_df, glb_allobs_df, 
         #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
         glb_models_df, dsp_models_df, glb_models_lst, glb_model_type,
         glb_sel_mdl, glb_sel_mdl_id,
         glb_fin_mdl, glb_fin_mdl_id,
        file=paste0(glb_out_pfx, "prdnew_dsk.RData"))

rm(submit_df, tmp_OOBobs_df)
## Warning in rm(submit_df, tmp_OOBobs_df): object 'tmp_OOBobs_df' not found
# tmp_replay_lst <- replay.petrisim(pn=glb_analytics_pn, 
#     replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs, 
#         "data.new.prediction")), flip_coord=TRUE)
# print(ggplot.petrinet(tmp_replay_lst[["pn"]]) + coord_flip())

glb_chunks_df <- myadd_chunk(glb_chunks_df, "display.session.info", major.inc=TRUE)
##                   label step_major step_minor    bgn    end elapsed
## 16     predict.data.new          9          0 92.340 96.276   3.937
## 17 display.session.info         10          0 96.277     NA      NA

Null Hypothesis (\(\sf{H_{0}}\)): mpg is not impacted by am_fctr.
The variance by am_fctr appears to be independent. #{r q1, cache=FALSE} # print(t.test(subset(cars_df, am_fctr == "automatic")$mpg, # subset(cars_df, am_fctr == "manual")$mpg, # var.equal=FALSE)$conf) # We reject the null hypothesis i.e. we have evidence to conclude that am_fctr impacts mpg (95% confidence). Manual transmission is better for miles per gallon versus automatic transmission.

##                      label step_major step_minor    bgn    end elapsed
## 11              fit.models          7          1 41.151 64.780  23.629
## 10              fit.models          7          0 24.088 41.151  17.063
## 12              fit.models          7          2 64.781 78.793  14.013
## 2             inspect.data          2          0 13.140 20.289   7.149
## 15       fit.data.training          8          1 87.582 92.339   4.758
## 14       fit.data.training          8          0 82.896 87.581   4.685
## 13              fit.models          7          3 78.794 82.895   4.101
## 16        predict.data.new          9          0 92.340 96.276   3.937
## 5         extract.features          3          0 21.454 22.799   1.345
## 3               scrub.data          2          1 20.290 21.385   1.096
## 8          select.features          5          0 23.158 23.765   0.608
## 1              import.data          1          0 12.683 13.140   0.457
## 9  partition.data.training          6          0 23.766 24.088   0.322
## 6             cluster.data          4          0 22.800 23.091   0.291
## 4           transform.data          2          2 21.386 21.453   0.067
## 7      manage.missing.data          4          1 23.092 23.158   0.066
##    duration
## 11   23.629
## 10   17.063
## 12   14.012
## 2     7.149
## 15    4.757
## 14    4.685
## 13    4.101
## 16    3.936
## 5     1.345
## 3     1.095
## 8     0.607
## 1     0.457
## 9     0.322
## 6     0.291
## 4     0.067
## 7     0.066
## [1] "Total Elapsed Time: 96.276 secs"

## R version 3.2.1 (2015-06-18)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.10.3 (Yosemite)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] tcltk     grid      parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] gdata_2.16.1        randomForest_4.6-10 arm_1.8-5          
##  [4] lme4_1.1-8          Matrix_1.2-1        MASS_7.3-41        
##  [7] rpart.plot_1.5.2    rpart_4.1-9         ROCR_1.0-7         
## [10] gplots_2.17.0       dplyr_0.4.2         plyr_1.8.3         
## [13] sqldf_0.4-10        RSQLite_1.0.0       DBI_0.3.1          
## [16] gsubfn_0.6-6        proto_0.3-10        reshape2_1.4.1     
## [19] caTools_1.17.1      doMC_1.3.3          iterators_1.0.7    
## [22] foreach_1.4.2       doBy_4.5-13         survival_2.38-2    
## [25] caret_6.0-47        ggplot2_1.0.1       lattice_0.20-31    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.11.6         class_7.3-12        gtools_3.5.0       
##  [4] assertthat_0.1      digest_0.6.8        R6_2.0.1           
##  [7] BradleyTerry2_1.0-6 chron_2.3-47        coda_0.17-1        
## [10] evaluate_0.7        e1071_1.6-4         lazyeval_0.1.10    
## [13] minqa_1.2.4         SparseM_1.6         car_2.0-25         
## [16] nloptr_1.0.4        rmarkdown_0.7       labeling_0.3       
## [19] splines_3.2.1       stringr_1.0.0       munsell_0.4.2      
## [22] compiler_3.2.1      mgcv_1.8-6          htmltools_0.2.6    
## [25] nnet_7.3-9          codetools_0.2-11    brglm_0.5-9        
## [28] bitops_1.0-6        nlme_3.1-120        gtable_0.1.2       
## [31] magrittr_1.5        formatR_1.2         scales_0.2.5       
## [34] KernSmooth_2.23-14  stringi_0.5-4       RColorBrewer_1.1-2 
## [37] tools_3.2.1         abind_1.4-3         pbkrtest_0.4-2     
## [40] yaml_2.1.13         colorspace_1.2-6    knitr_1.10.5       
## [43] quantreg_5.11